metontiime and qiime2

[dinavb]

Hi, I want to use metontiime in order to prepare the 16s reads from nanoporre to analysis in qiime 2 ( The final goal is to receive alpha and beta diversity and analysis of qiime 2 and not only the analysis available with epi2me). We understand from qiime 2 that there are problems with using nanopore data: adapters need to be removed, barcodes need to be removed, denoising. In addition, the qiime2 database is of short reads, so we need to trim the nanopore long reads only to the V3 V4 regions . Is there any script performing all those in order to prepare the ONT data for qiime 2 analysis and how are the results in qiime 2 after all those manipulations? Thank you!

[MaestSi]

Hi, base-calling, demultiplexing, adapters removal and quality filtering are performed by the MetONTIIME pipeline. Databases mentioned in the README (e.g. Silva or NCBI 16S Bacterial) include the full 16S gene, so you don't need to trim your samples to V3-V4 regions. Once you have run the pipeline, you can either choose between clustering reads and performing a phylogenetic diversity analysis (e.g. with Evaluate_diversity.sh script), or to perform a non-phylogenetic analysis on frequency tables collapsed at the desired taxonomic level. Does this help? Simone

[dinavb]

Thank you! Can you give me some instructions how to begin? What do I need in order to begin with ONT data and end with alpha and beta diversity and the kind of analysis done by qiime2?

On Tue, Nov 24, 2020 at 2:12 PM Simone Maestri notifications@github.com wrote:

Hi, base-calling, demultiplexing, adapters removal and quality filtering are performed by the MetONTIIME pipeline. Databases mentioned in the README (e.g. Silva or NCBI 16S Bacterial) include the full 16S gene, so you don't need to trim your samples to V3-V4 regions. Once you have run the pipeline, you can either choose between clustering reads and performing a phylogenetic diversity analysis (e.g. with Evaluate_diversity.sh script), or to perform a non-phylogenetic analysis on frequency tables collapsed at the desired taxonomic level. Does this help? Simone

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[MaestSi]

If you start with raw fast5 files you can follow the instructions in the README. Namely, perform installation and configuration, import a database of interest and run the full analysis with Launch_MinION_mobile_lab.sh. After the analysis is finished, you can decide if you want to perform non-phylogenetic analyses, e.g. with

qiime diversity beta --i-table collapsed_feature_tables/table_collapsed_absfreq_level5.qza  --p-metric braycurtis --o-distance-matrix unweighted_unifrac_distance_matrix_level5.qza
qiime tools export --input-path unweighted_unifrac_distance_matrix_level5.qza --output-path .

or to run a phylogenetic-based diversity analysis using the Evaluate_diversity.sh script. For deciding which approach is more suitable you may refer to QIIME2 website, which has a Docs section (with many tutorials) and an hectic Forum. If you encounter any issues or have specific questions, please don't hesitate to ask.

[dinavb]

I begin with fastq files, already demultiplexed by barcodes.

On Tue, Nov 24, 2020 at 3:01 PM Simone Maestri notifications@github.com wrote:

If you start with raw fast5 files you can follow the instructions in the README. Namely, perform installation and configuration, import a database of interest and run the full analysis with Launch_MinION_mobile_lab.sh. After the analysis is finished, you can decide if you want to perform non-phylogenetic analyses, e.g. with

qiime diversity beta --i-table collapsed_feature_tables/table_collapsed_absfreq_level5.qza --p-metric braycurtis --o-distance-matrix unweighted_unifrac_distance_matrix_level5.qza qiime tools export --input-path unweighted_unifrac_distance_matrix_level5.qza --output-path .

or to run a phylogenetic-based diversity analysis using the Evaluate_diversity.sh script. For deciding which approach is more suitable you may refer to QIIME2 website https://qiime2.org/, which has a Docs section (with many tutorials) and an hectic Forum. If you encounter any issues or have specific questions, please don't hesitate to ask.

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[MaestSi]

So you probably already have the adapters and the barcodes and the PCR primers trimmed, if you used the "--trim_barcodes" option of guppy_barcoder. You may also already have your sequences filtered by quality. If this is not the case I advise running the full workflow starting from fast5 files. In case you already have preprocessed fastq files, compress fastq files to fastq.gz with:

FASTQ_DIR="/path/to/dir/with/fastq"
for fastq_file in $(find $FASTQ_DIR -maxdepth 1 | grep "\.fastq$"); do
  gzip $fastq_file ;
done

Then, if you have your set of fastq.gz files run taxonomic analysis following "Starting analysis from fastq.gz files" section, after installation and configuration.

[dinavb]

What about alpha and beta diversity between two samples or sets of samples?

On Tue, Nov 24, 2020 at 3:58 PM Simone Maestri notifications@github.com wrote:

So you probably already have the adapters and the barcodes and the PCR primers trimmed, if you used the "--trim_barcodes" option of guppy_barcoder. You may also already have your sequences filtered by quality. If this is not the case I advise running the full workflow starting from fast5 files. In case you already have preprocessed fastq files, compress fastq files to fastq.gz with:

FASTQ_DIR="/path/to/dir/with/fastq" for fastq_file in $(find $FASTQ_DIR -maxdepth 1 | grep ".fastq$"); do gzip $fastq_file ; done

Then, if you have your set of fastq.gz files run taxonomic analysis following "Starting analysis from fastq.gz files" section, after installation and configuration.

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[MaestSi]

You first have to choose between phylogenetic or non-phylogenetic methods. The first step for using a phylogeny-based method is to pick representative sequences (by clustering), building a phylogenetic tree by aligning the representative sequences to each other and then computing alpha and beta diversity metrics. All these steps are implemented in the Evaluate_diversity.sh script, you can find instructions for running it in the README. If you want to use a non-phylogenetic method, you just have to use qiime diversity beta or qiime diversity alpha (use qiime diversity --help for seeing the options), and specifying as --i-table the absolute frequency table collapsed at a desired taxonomic level. In particular, if you previously ran the pipeline, you should have a folder called collapsed_feature_tables in the analysis folder, containing a set of files named table_collapsed_absfreq_levelX.qza. The level represents the depth of the taxonomic assignment, from kingdom to species. In this case (differently to Illumina-based analyses) you need to use a collapsed feature table, because if you use the uncollapsed table table.qza, you are going to get diversity equal to 1 in all cases, due to the error rate causing each sequence to be seen as an amplicon sequence variant (therefore 1 error in the sequence -> 1 different ASV). I suggest reading the following tutorials:

• https://forum.qiime2.org/t/alpha-and-beta-diversity-explanations-and-commands/2282
• https://otagoedna.github.io/getting_started_with_qiime2/diversity_analyses/diversity_analyses.html
• https://docs.qiime2.org/2020.8/tutorials/moving-pictures/

[MaestSi]

I'll close the issue for now, if you have specific questions feel free to reopen it. Simone

[dinavb]

HI I tried and received the following error:

(qiime2-2020.8) qiime2@qiime2core2020-8:~$ conda activate MetONTIIME_env dir (MetONTIIME_env) qiime2@qiime2core2020-8:~$ dir Desktop Music Silva_132_release.zip __MACOSX miniconda.sh Documents Pictures Silva_132_release.zip.1 barcodes nohup.out Downloads Public Templates examples.desktop silva_132_99_16S_sequence.qza MetONTIIME SILVA_132_QIIME_release Videos miniconda silva_132_99_16S_taxonomy.qza (MetONTIIME_env) qiime2@qiime2core2020-8:~$ nohup ./MetONTIIME/MetONTIIME.sh ./barcodes ./silva_132_99_16S_sequence.qza ./silva_132_99_16S_taxonomy.qza 5 Blast 1 1 1 nohup: ignoring input and appending output to 'nohup.out'

On Wed, Nov 25, 2020 at 12:25 PM Simone Maestri notifications@github.com wrote:

Closed #20 https://github.com/MaestSi/MetONTIIME/issues/20.

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[MaestSi]

Hi, this doesn't look like an error, it just says that the job is running in background and writing the standard output and the standard error to the file nohup.out, which you can read with less or cat commands, among many others (and, in case, share with me for understanding what is causing the issue, if there are any). Moreover, I saw you are using value 1 for parameters MAX_ACCEPTS, QUERY_COV and ID_THR. I would suggest using, for example, default parameters 3 0.8 0.85 (as reported in the config file), since requiring a query coverage and an alignment identity of 100% you are probably going to get no taxonomy assignments (no Nanopore reads are identical to a sequence in the database due to the error rate). Finally, I am not sure the pipeline can run on MACOS, I just tested it on Ubuntu. Simone

[dinavb]

Dear Simone, We tried with the parameters you wrote. We receive :nohup: ignoring input and appending output to 'nohup.out' I attach also the file nohup.out. Please advise

On Sun, Nov 29, 2020 at 4:25 PM Simone Maestri notifications@github.com wrote:

Hi, this doesn't look like an error, it just says that the job is running in background and writing the standard output and the standard error to the file nohup.out, which you can read with less or cat commands, among many others (and, in case, share with me for understanding what is causing the issue, if there are any). Moreover, I saw you are using value 1 for parameters MAX_ACCEPTS, QUERY_COV and ID_THR. I would suggest using, for example, default parameters 3 0.8 0.85 (as reported in the config file), since requiring a query coverage and an alignment identity of 100% you are probably going to get no taxonomy assignments (no Nanopore reads are identical to a sequence in the database due to the error rate). Finally, I am not sure the pipeline can run on MACOS, I just tested it on Ubuntu. Simone

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[MaestSi]

nohup: ignoring input and appending output to 'nohup.out'

is the standard message you get when you start a job in background with nohup, it is not an error. I can't see the nohup.out file attached, could you send it again?

[dinavb]

Trying to attach again

On Mon, Nov 30, 2020 at 10:23 AM Simone Maestri notifications@github.com wrote:

nohup: ignoring input and appending output to 'nohup.out'

is the standard message you get when you start a job in background with nohup, it is not an error. I can't see the nohup.out file attached, could you send it again?

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[MaestSi]

I think you need to save the file with .txt extension, otherwise it is not going to be uploaded.

[dinavb]

Trying again with txt

On Mon, Nov 30, 2020 at 11:14 AM Simone Maestri notifications@github.com wrote:

I think you need to save the file with .txt extension, otherwise it is not going to be uploaded.

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Usage: qiime tools import [OPTIONS]

Import data to create a new QIIME 2 Artifact. See https://docs.qiime2.org/ for usage examples and details on the file types and associated semantic types that can be imported.

Options: --type TEXT The semantic type of the artifact that will be created upon importing. Use --show-importable-types to see what importable semantic types are available in the current deployment. [required] --input-path PATH Path to file or directory that should be imported. [required] --output-path ARTIFACT Path where output artifact should be written. [required] --input-format TEXT The format of the data to be imported. If not provided, data must be in the format expected by the semantic type provided via --type. --show-importable-types Show the semantic types that can be supplied to --type to import data into an artifact. --show-importable-formats Show formats that can be supplied to --input-format to import data into an artifact. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': Path 'barcodes/manifest.txt' does not exist. Usage: qiime vsearch dereplicate-sequences [OPTIONS]

Dereplicate sequence data and create a feature table and feature representative sequences. Feature identifiers in the resulting artifacts will be the sha1 hash of the sequence defining each feature. If clustering of features into OTUs is desired, the resulting artifacts can be passed to the clusterfeatures* methods in this plugin.

Inputs: --i-sequences ARTIFACT SampleData[Sequences] | SampleData[SequencesWithQuality] | SampleData[JoinedSequencesWithQuality] The sequences to be dereplicated. [required] Parameters: --p-derep-prefix / --p-no-derep-prefix Merge sequences with identical prefixes. If a sequence is identical to the prefix of two or more longer sequences, it is clustered with the shortest of them. If they are equally long, it is clustered with the most abundant. [default: False] Outputs: --o-dereplicated-table ARTIFACT FeatureTable[Frequency] The table of dereplicated sequences. [required] --o-dereplicated-sequences ARTIFACT FeatureData[Sequence] The dereplicated sequences. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-sequences': 'sequences.qza' is not a valid filepath Usage: qiime vsearch cluster-features-de-novo [OPTIONS]

Given a feature table and the associated feature sequences, cluster the features based on user-specified percent identity threshold of their sequences. This is not a general-purpose de novo clustering method, but rather is intended to be used for clustering the results of quality- filtering/dereplication methods, such as DADA2, or for re-clustering a FeatureTable at a lower percent identity than it was originally clustered at. When a group of features in the input table are clustered into a single feature, the frequency of that single feature in a given sample is the sum of the frequencies of the features that were clustered in that sample. Feature identifiers and sequences will be inherited from the centroid feature of each cluster. See the vsearch documentation for details on how sequence clustering is performed.

Inputs: --i-sequences ARTIFACT FeatureData[Sequence] The sequences corresponding to the features in table. [required] --i-table ARTIFACT FeatureTable[Frequency] The feature table to be clustered. [required] Parameters: --p-perc-identity PROPORTION Range(0, 1, inclusive_start=False, inclusive_end=True) The percent identity at which clustering should be performed. This parameter maps to vsearch's --id parameter. [required] --p-threads INTEGER Range(0, 256, inclusive_end=True) The number of threads to use for computation. Passing 0 will launch one thread per CPU core. [default: 1] Outputs: --o-clustered-table ARTIFACT FeatureTable[Frequency] The table following clustering of features. [required] --o-clustered-sequences ARTIFACT FeatureData[Sequence] Sequences representing clustered features. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1?) --p-threads option requires an argument rm: cannot remove 'table_tmp.qza': No such file or directory rm: cannot remove 'rep-seqs_tmp.qza': No such file or directory Usage: qiime demux summarize [OPTIONS]

Summarize counts per sample for all samples, and generate interactive positional quality plots based on n randomly selected sequences.

Inputs: --i-data ARTIFACT SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality] The demultiplexed sequences to be summarized. [required] Parameters: --p-n INTEGER The number of sequences that should be selected at random for quality score plots. The quality plots will present the average positional qualities across all of the sequences selected. If input sequences are paired end, plots will be generated for both forward and reverse reads for the same n sequences. [default: 10000] Outputs: --o-visualization VISUALIZATION [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-data': 'sequences.qza' is not a valid filepath There was an issue with loading the file silva_132_99_16S_sequence.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): silva_132_99_16S_sequence.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime feature-table tabulate-seqs [OPTIONS]

Generate tabular view of feature identifier to sequence mapping, including links to BLAST each sequence against the NCBI nt database.

Inputs: --i-data ARTIFACT FeatureData[Sequence | AlignedSequence] The feature sequences to be tabulated. [required] Outputs: --o-visualization VISUALIZATION [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-data': 'rep-seqs.qza' is not a valid filepath Classifier is not supported (choose between Blast and Vsearch); running default classifier Blast Usage: qiime feature-classifier classify-consensus-blast [OPTIONS]

Assign taxonomy to query sequences using BLAST+. Performs BLAST+ local alignment between query and reference_reads, then assigns consensus taxonomy to each query sequence from among maxaccepts hits, min_consensus of which share that taxonomic assignment. Note that maxaccepts selects the first N hits with > perc_identity similarity to query, not the top N matches. For top N hits, use classify-consensus-vsearch.

Inputs: --i-query ARTIFACT FeatureData[Sequence] Sequences to classify taxonomically. [required] --i-reference-reads ARTIFACT FeatureData[Sequence] reference sequences. [required] --i-reference-taxonomy ARTIFACT FeatureData[Taxonomy] reference taxonomy labels. [required] Parameters: --p-maxaccepts INTEGER Maximum number of hits to keep for each query. Must Range(1, None) be in range [1, infinity]. BLAST will choose the first N hits in the reference database that exceed perc-identity similarity to query. [default: 10] --p-perc-identity PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if percent identity to query is lower. Must be in range [0.0, 1.0]. [default: 0.8] --p-query-cov PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if query alignment coverage per high-scoring pair is lower. Note: this uses blastn's qcov_hsp_perc parameter, and may not behave identically to the query-cov parameter used by classify-consensus-vsearch. Must be in range [0.0, 1.0]. [default: 0.8] --p-strand TEXT Choices('both', 'plus', 'minus') Align against reference sequences in forward ("plus"), reverse ("minus"), or both directions ("both"). [default: 'both'] --p-evalue NUMBER BLAST expectation value (E) threshold for saving hits. [default: 0.001] --p-min-consensus NUMBER Range(0.5, 1.0, inclusive_start=False, inclusive_end=True) Minimum fraction of assignments must match top hit to be accepted as consensus assignment. Must be in range (0.5, 1.0]. [default: 0.51] --p-unassignable-label TEXT [default: 'Unassigned'] Outputs: --o-classification ARTIFACT FeatureData[Taxonomy] Taxonomy classifications of query sequences. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2?) --i-reference-taxonomy option requires an argument (2/2?) --p-query-cov option requires an argument There was an issue with loading the file taxonomy.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): taxonomy.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

There was an issue with loading the file silva_132_99_16S_sequence.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): silva_132_99_16S_sequence.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime taxa filter-table [OPTIONS]

This method filters features from a table based on their taxonomic annotations. Features can be retained in the resulting table by specifying one or more include search terms, and can be filtered out of the resulting table by specifying one or more exclude search terms. If both include and exclude are provided, the inclusion critera will be applied before the exclusion critera. Either include or exclude terms (or both) must be provided. Any samples that have a total frequency of zero after filtering will be removed from the resulting table.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be filtered. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations for features that are not present in the feature table will be ignored. [required] Parameters: --p-include TEXT One or more search terms that indicate which taxa should be included in the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, all taxa will be included. [optional] --p-exclude TEXT One or more search terms that indicate which taxa should be excluded from the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, no taxa will be excluded. [optional] --p-query-delimiter TEXT The string used to delimit multiple search terms provided to include or exclude. This parameter should only need to be modified if the default delimiter (a comma) is used in the provided taxonomic annotations. [default: ','] --p-mode TEXT Choices('exact', 'contains') Mode for determining if a search term matches a taxonomic annotation. "contains" requires that the annotation has the term as a substring; "exact" requires that the annotation is a perfect match to a search term. [default: 'contains'] Outputs: --o-filtered-table ARTIFACT FeatureTable[Frequency] The taxonomy-filtered feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file silva_132_99_16S_sequence.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): silva_132_99_16S_sequence.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level1.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level1.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level1.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level1.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS]

Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level1.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level1.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level1.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level1.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level1.biom' does not exist. cat: feature-table_absfreq_level1.tsv: No such file or directory cat: feature-table_absfreq_level1.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level2.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level2.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level2.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level2.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS]

Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level2.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level2.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level2.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level2.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level2.biom' does not exist. cat: feature-table_absfreq_level2.tsv: No such file or directory cat: feature-table_absfreq_level2.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level3.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level3.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level3.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level3.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS]

Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level3.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level3.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level3.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level3.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level3.biom' does not exist. cat: feature-table_absfreq_level3.tsv: No such file or directory cat: feature-table_absfreq_level3.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level4.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level4.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level4.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level4.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS]

Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level4.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level4.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level4.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level4.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level4.biom' does not exist. cat: feature-table_absfreq_level4.tsv: No such file or directory cat: feature-table_absfreq_level4.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level5.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level5.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level5.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level5.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS]

Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level5.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level5.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level5.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level5.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level5.biom' does not exist. cat: feature-table_absfreq_level5.tsv: No such file or directory cat: feature-table_absfreq_level5.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level6.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level6.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level6.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level6.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS]

Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level6.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level6.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level6.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level6.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level6.biom' does not exist. cat: feature-table_absfreq_level6.tsv: No such file or directory cat: feature-table_absfreq_level6.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level7.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level7.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level7.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level7.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS]

Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level7.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level7.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level7.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qii

[MaestSi]

Only the first error is relevant, all the following errors are only a consequence. So, it looks like the import of some files failed. For further debugging I need to know which file you have in the working directory and the exact command you used. But I point out again that the issue may be due to your operating system different from Ubuntu.

[dinavb]

I used the command: nohup ./MetONTIIME/MetONTIIME.sh "./barcodes" ./silva_132_99_16S_sequence.qza ./silva_132_99_16S_taxonomy.qza 5 Blast 3 0.8 0.85

The files in the directory: (MetONTIIME_env) qiime2@qiime2core2020-8:~$ dir Desktop SILVA_132_QIIME_release examples.desktop Documents Silva_132_release.zip miniconda Downloads Silva_132_release.zip.1 miniconda.sh MetONTIIME Templates nohup.out Music Videos silva_132_99_16S_sequence.qza Pictures __MACOSX silva_132_99_16S_taxonomy.qza

we do use Ubunto

On Mon, Nov 30, 2020 at 12:06 PM Simone Maestri notifications@github.com wrote:

Only the first error is relevant, all the following errors are only a consequence. So, it looks like the import of some files failed. For further debugging I need to know which file you have in the working directory and the exact command you used. But I point out again that the issue may be due to your operating system different from Ubuntu.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/MaestSi/MetONTIIME/issues/20#issuecomment-735686664, or unsubscribe https://github.com/notifications/unsubscribe-auth/AR34USRVZSKXAK3JWKL7TITSSNVDNANCNFSM4UAYZG7Q .

[MaestSi]

It looks like you don't have any "./barcodes" directory, do you? What files do you have in that folder?

[dinavb]

In the barcodes folder I have the compressed fastq files of several different samples.

On Mon, Nov 30, 2020 at 2:42 PM Simone Maestri notifications@github.com wrote:

It looks like you don't have any "./barcodes" directory, do you? What files do you have in that folder?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/MaestSi/MetONTIIME/issues/20#issuecomment-735762954, or unsubscribe https://github.com/notifications/unsubscribe-auth/AR34USW4WFVOHIVZR6IJY53SSOHKHANCNFSM4UAYZG7Q .

[MaestSi]

Based on the instruction suggested in the README: nohup ./MetONTIIME.sh <working_dir> <metadata file> <sequences qiime2 artifact> <taxonomy qiime2 artifact> <threads> <taxonomic classifier> <max accepts> <query coverage> <id thr> & it looks like you did not specify any metadata file. If the file doesn't exist yet, it is created by the pipeline, but it is compulsory to specify where you want it to be created. For example try with: nohup ./MetONTIIME/MetONTIIME.sh ./barcodes ./sample-metadata.tsv ./silva_132_99_16S_sequence.qza ./silva_132_99_16S_taxonomy.qza 5 Blast 3 0.8 0.85 & P.s.: Blast is single-threaded in QIIME2 implementation, for speeding up the analysis I suggest specifying Vsearch instead of Blast.

[dinavb]

I tried it again with your suggestions. Attached is the output I received now. Thank you!

On Mon, Nov 30, 2020 at 4:52 PM Simone Maestri notifications@github.com wrote:

Based on the instruction suggested in the README: nohup ./MetONTIIME.sh <sequences qiime2 artifact> <max accepts> & it looks like you did not specify any metadata file. If the file doesn't exist yet, it is created by the pipeline, but it is compulsory to specify where you want it to be created. For example try with: nohup ./MetONTIIME/MetONTIIME.sh ./barcodes ./sample-metadata.tsv ./silva_132_99_16S_sequence.qza ./silva_132_99_16S_taxonomy.qza 5 Blast 3 0.8 0.85 & P.s.: Blast is single-threaded in QIIME2 implementation, for speeding up the analysis I suggest specifying Vsearch instead of Blast.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/MaestSi/MetONTIIME/issues/20#issuecomment-735832969, or unsubscribe https://github.com/notifications/unsubscribe-auth/AR34USVIBQ37WO25ULFE2CTSSOWR3ANCNFSM4UAYZG7Q .

Usage: qiime tools import [OPTIONS]

Import data to create a new QIIME 2 Artifact. See https://docs.qiime2.org/ for usage examples and details on the file types and associated semantic types that can be imported.

Options: --type TEXT The semantic type of the artifact that will be created upon importing. Use --show-importable-types to see what importable semantic types are available in the current deployment. [required] --input-path PATH Path to file or directory that should be imported. [required] --output-path ARTIFACT Path where output artifact should be written. [required] --input-format TEXT The format of the data to be imported. If not provided, data must be in the format expected by the semantic type provided via --type. --show-importable-types Show the semantic types that can be supplied to --type to import data into an artifact. --show-importable-formats Show formats that can be supplied to --input-format to import data into an artifact. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': Path './barcodes/manifest.txt' does not exist. Usage: qiime vsearch dereplicate-sequences [OPTIONS]

Dereplicate sequence data and create a feature table and feature representative sequences. Feature identifiers in the resulting artifacts will be the sha1 hash of the sequence defining each feature. If clustering of features into OTUs is desired, the resulting artifacts can be passed to the clusterfeatures* methods in this plugin.

Inputs: --i-sequences ARTIFACT SampleData[Sequences] | SampleData[SequencesWithQuality] | SampleData[JoinedSequencesWithQuality] The sequences to be dereplicated. [required] Parameters: --p-derep-prefix / --p-no-derep-prefix Merge sequences with identical prefixes. If a sequence is identical to the prefix of two or more longer sequences, it is clustered with the shortest of them. If they are equally long, it is clustered with the most abundant. [default: False] Outputs: --o-dereplicated-table ARTIFACT FeatureTable[Frequency] The table of dereplicated sequences. [required] --o-dereplicated-sequences ARTIFACT FeatureData[Sequence] The dereplicated sequences. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-sequences': 'sequences.qza' is not a valid filepath Usage: qiime vsearch cluster-features-de-novo [OPTIONS]

Given a feature table and the associated feature sequences, cluster the features based on user-specified percent identity threshold of their sequences. This is not a general-purpose de novo clustering method, but rather is intended to be used for clustering the results of quality- filtering/dereplication methods, such as DADA2, or for re-clustering a FeatureTable at a lower percent identity than it was originally clustered at. When a group of features in the input table are clustered into a single feature, the frequency of that single feature in a given sample is the sum of the frequencies of the features that were clustered in that sample. Feature identifiers and sequences will be inherited from the centroid feature of each cluster. See the vsearch documentation for details on how sequence clustering is performed.

Inputs: --i-sequences ARTIFACT FeatureData[Sequence] The sequences corresponding to the features in table. [required] --i-table ARTIFACT FeatureTable[Frequency] The feature table to be clustered. [required] Parameters: --p-perc-identity PROPORTION Range(0, 1, inclusive_start=False, inclusive_end=True) The percent identity at which clustering should be performed. This parameter maps to vsearch's --id parameter. [required] --p-threads INTEGER Range(0, 256, inclusive_end=True) The number of threads to use for computation. Passing 0 will launch one thread per CPU core. [default: 1] Outputs: --o-clustered-table ARTIFACT FeatureTable[Frequency] The table following clustering of features. [required] --o-clustered-sequences ARTIFACT FeatureData[Sequence] Sequences representing clustered features. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-sequences': 'rep-seqs_tmp.qza' is not a valid filepath (2/2) Invalid value for '--i-table': 'table_tmp.qza' is not a valid filepath rm: cannot remove 'table_tmp.qza': No such file or directory rm: cannot remove 'rep-seqs_tmp.qza': No such file or directory Usage: qiime demux summarize [OPTIONS]

Summarize counts per sample for all samples, and generate interactive positional quality plots based on n randomly selected sequences.

Inputs: --i-data ARTIFACT SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality] The demultiplexed sequences to be summarized. [required] Parameters: --p-n INTEGER The number of sequences that should be selected at random for quality score plots. The quality plots will present the average positional qualities across all of the sequences selected. If input sequences are paired end, plots will be generated for both forward and reverse reads for the same n sequences. [default: 10000] Outputs: --o-visualization VISUALIZATION [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-data': 'sequences.qza' is not a valid filepath There was an issue with loading the file ./sample-metadata.tsv as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): ./sample-metadata.tsv

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime feature-table tabulate-seqs [OPTIONS]

Generate tabular view of feature identifier to sequence mapping, including links to BLAST each sequence against the NCBI nt database.

Inputs: --i-data ARTIFACT FeatureData[Sequence | AlignedSequence] The feature sequences to be tabulated. [required] Outputs: --o-visualization VISUALIZATION [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-data': 'rep-seqs.qza' is not a valid filepath Usage: qiime feature-classifier classify-consensus-vsearch [OPTIONS]

Assign taxonomy to query sequences using VSEARCH. Performs VSEARCH global alignment between query and reference_reads, then assigns consensus taxonomy to each query sequence from among maxaccepts top hits, min_consensus of which share that taxonomic assignment. Unlike classify- consensus-blast, this method searches the entire reference database before choosing the top N hits, not the first N hits.

Inputs: --i-query ARTIFACT FeatureData[Sequence] Sequences to classify taxonomically. [required] --i-reference-reads ARTIFACT FeatureData[Sequence] reference sequences. [required] --i-reference-taxonomy ARTIFACT FeatureData[Taxonomy] reference taxonomy labels. [required] Parameters: --p-maxaccepts VALUE Int % Range(1, None) | Str % Choices('all') Maximum number of hits to keep for each query. Set to "all" to keep all hits > perc-identity similarity. Note that if strand=both, maxaccepts will keep N hits for each direction (if searches in the opposite direction yield results that exceed the minimum perc-identity). In those cases use maxhits to control the total number of hits returned. This option works in pair with maxrejects. The search process sorts target sequences by decreasing number of k-mers they have in common with the query sequence, using that information as a proxy for sequence similarity. After pairwise alignments, if the first target sequence passes the acceptation criteria, it is accepted as best hit and the search process stops for that query. If maxaccepts is set to a higher value, more hits are accepted. If maxaccepts and maxrejects are both set to "all", the complete database is searched. [default: 10] --p-perc-identity PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if percent identity to query is lower. [default: 0.8] --p-query-cov PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if query alignment coverage per high-scoring pair is lower. [default: 0.8] --p-strand TEXT Choices('both', 'plus') Align against reference sequences in forward ("plus") or both directions ("both"). [default: 'both'] --p-min-consensus NUMBER Range(0.5, 1.0, inclusive_start=False, inclusive_end=True) Minimum fraction of assignments must match top hit to be accepted as consensus assignment. [default: 0.51] --p-unassignable-label TEXT [default: 'Unassigned'] --p-search-exact / --p-no-search-exact Search for exact full-length matches to the query sequences. Only 100% exact matches are reported and this command is much faster than the default. If True, the perc-identity and query-cov settings are ignored. Note: query and reference reads must be trimmed to the exact same DNA locus (e.g., primer site) because only exact matches will be reported. [default: False] --p-top-hits-only / --p-no-top-hits-only Only the top hits between the query and reference sequence sets are reported. For each query, the top hit is the one presenting the highest percentage of identity. Multiple equally scored top hits will be used for consensus taxonomic assignment if maxaccepts is greater than 1. [default: False] --p-maxhits VALUE Int % Range(1, None) | Str % Choices('all') Maximum number of hits to show once the search is terminated. [default: 'all'] --p-maxrejects VALUE Int % Range(1, None) | Str % Choices('all') Maximum number of non-matching target sequences to consider before stopping the search. This option works in pair with maxaccepts (see maxaccepts description for details). [default: 'all'] --p-output-no-hits / --p-no-output-no-hits Report both matching and non-matching queries. WARNING: always use the default setting for this option unless if you know what you are doing! If you set this option to False, your sequences and feature table will need to be filtered to exclude unclassified sequences, otherwise you may run into errors downstream from missing feature IDs. [default: True] --p-weak-id PROPORTION Range(0.0, 1.0, inclusive_end=True) Show hits with percentage of identity of at least N, without terminating the search. A normal search stops as soon as enough hits are found (as defined by maxaccepts, maxrejects, and perc-identity). As weak-id reports weak hits that are not deduced from maxaccepts, high perc-identity values can be used, hence preserving both speed and sensitivity. Logically, weak-id must be smaller than the value indicated by perc-identity, otherwise this option will be ignored. [default: 0.0] --p-threads INTEGER Number of threads to use for job parallelization. Range(1, None) [default: 1] Outputs: --o-classification ARTIFACT FeatureData[Taxonomy] The resulting taxonomy classifications. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/3) Invalid value for '--i-query': 'rep-seqs.qza' is not a valid filepath (2/3) Invalid value for '--i-reference-reads': './silva_132_99_16S_sequence.qza' is not a valid filepath (3/3) Invalid value for '--i-reference-taxonomy': './silva_132_99_16S_taxonomy.qza' is not a valid filepath There was an issue with loading the file taxonomy.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): taxonomy.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

There was an issue with loading the file ./sample-metadata.tsv as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): ./sample-metadata.tsv

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime taxa filter-table [OPTIONS]

This method filters features from a table based on their taxonomic annotations. Features can be retained in the resulting table by specifying one or more include search terms, and can be filtered out of the resulting table by specifying one or more exclude search terms. If both include and exclude are provided, the inclusion critera will be applied before the exclusion critera. Either include or exclude terms (or both) must be provided. Any samples that have a total frequency of zero after filtering will be removed from the resulting table.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be filtered. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations for features that are not present in the feature table will be ignored. [required] Parameters: --p-include TEXT One or more search terms that indicate which taxa should be included in the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, all taxa will be included. [optional] --p-exclude TEXT One or more search terms that indicate which taxa should be excluded from the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, no taxa will be excluded. [optional] --p-query-delimiter TEXT The string used to delimit multiple search terms provided to include or exclude. This parameter should only need to be modified if the default delimiter (a comma) is used in the provided taxonomic annotations. [default: ','] --p-mode TEXT Choices('exact', 'contains') Mode for determining if a search term matches a taxonomic annotation. "contains" requires that the annotation has the term as a substring; "exact" requires that the annotation is a perfect match to a search term. [default: 'contains'] Outputs: --o-filtered-table ARTIFACT FeatureTable[Frequency] The taxonomy-filtered feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file ./sample-metadata.tsv as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): ./sample-metadata.tsv

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level1.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level1.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level1.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level1.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS]

Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level1.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level1.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level1.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level1.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level1.biom' does not exist. cat: feature-table_absfreq_level1.tsv: No such file or directory cat: feature-table_absfreq_level1.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level2.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level2.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level2.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level2.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS]

Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level2.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level2.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level2.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level2.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level2.biom' does not exist. cat: feature-table_absfreq_level2.tsv: No such file or directory cat: feature-table_absfreq_level2.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level3.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level3.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level3.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level3.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS]

Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level3.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level3.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level3.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level3.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level3.biom' does not exist. cat: feature-table_absfreq_level3.tsv: No such file or directory cat: feature-table_absfreq_level3.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level4.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level4.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level4.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level4.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS]

Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level4.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level4.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level4.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level4.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level4.biom' does not exist. cat: feature-table_absfreq_level4.tsv: No such file or directory cat: feature-table_absfreq_level4.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level5.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level5.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level5.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level5.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS]

Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level5.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level5.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level5.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level5.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level5.biom' does not exist. cat: feature-table_absfreq_level5.tsv: No such file or directory cat: feature-table_absfreq_level5.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level6.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level6.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level6.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level6.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS]

Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level6.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level6.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level6.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level6.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level6.biom' does not exist. cat: feature-table_absfreq_level6.tsv: No such file or directory cat: feature-table_absfreq_level6.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be igno

[MaestSi]

The relevant error I see is:

Invalid value for '--input-path': Path './barcodes/manifest.txt' does not exist.

Is there a file named manifest.txt inside ./barcodes directory? If yes, please post here its content. I would suggest specifying the full path to the files (and not the relative paths). Moreover, are you sure you have writing permissions in the barcodes folder?

[dinavb]

Yes, there is manifest.txt in the barcodes directory. Attached.

On Mon, Nov 30, 2020 at 5:48 PM Simone Maestri notifications@github.com wrote:

The relevant error I see is:

Invalid value for '--input-path': Path './barcodes/manifest.txt' does not exist.

Is there a file named manifest.txt inside ./barcodes directory? If yes, please post here its content. I would suggest specifying the full path to the files (and not the relative paths). Moreover, are you sure you have writing permissions in the barcodes folder?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/MaestSi/MetONTIIME/issues/20#issuecomment-735869129, or unsubscribe https://github.com/notifications/unsubscribe-auth/AR34USV2TJ5WRNX6CA6XUUDSSO5GBANCNFSM4UAYZG7Q .

sample-id absolute-filepath barcode04 /home/qiime2/barcodes/barcode04.fastq.gz barcode07 /home/qiime2/barcodes/barcode07.fastq.gz barcode02 /home/qiime2/barcodes/barcode02.fastq.gz barcode06 /home/qiime2/barcodes/barcode06.fastq.gz barcode05 /home/qiime2/barcodes/barcode05.fastq.gz

[MaestSi]

This is strange, because the error message says the file doesn't exist. So, please, delete that file and be sure that in the barcodes directory there are only the files of interest. Then rerun the analysis but specifying the full path to the files and please, if it stops with errors, report the content of the manifest.txt file, sample-metadata.tsv file and the beginning of the nohup.out file (the first error). Thanks

[dinavb]

I rerun it using the full pathways : (MetONTIIME_env) qiime2@qiime2core2020-8:~$ nohup ./MetONTIIME/MetONTIIME.sh /home/qiime2/barcodes /home/sample-metadata.tsv /home/silva_132_99_16S_sequence.qza /home/silva_132_99_16S_taxonomy.qza 5 Vsearch 3 0.8 0.85

This time it took much longer until it ended, but still it seems to have errors. i attach the files.

On Mon, Nov 30, 2020 at 6:03 PM Simone Maestri notifications@github.com wrote:

This is strange, because the error message says the file doesn't exist. So, please, delete that file and be sure that in the barcodes directory there are only the files of interest. Then rerun the analysis but specifying the full path to the files and please, if it stops with errors, report the content of the manifest.txt file, sample-metadata.tsv file and the beginning of the nohup.out file (the first error). Thanks

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/MaestSi/MetONTIIME/issues/20#issuecomment-735878371, or unsubscribe https://github.com/notifications/unsubscribe-auth/AR34USTGRU4LZAL7IAQM773SSO657ANCNFSM4UAYZG7Q .

sample-id absolute-filepath barcode04 /home/qiime2/barcodes/barcode04.fastq.gz barcode07 /home/qiime2/barcodes/barcode07.fastq.gz barcode02 /home/qiime2/barcodes/barcode02.fastq.gz barcode06 /home/qiime2/barcodes/barcode06.fastq.gz barcode05 /home/qiime2/barcodes/barcode05.fastq.gz

Usage: qiime tools import [OPTIONS]

Import data to create a new QIIME 2 Artifact. See https://docs.qiime2.org/ for usage examples and details on the file types and associated semantic types that can be imported.

Options: --type TEXT The semantic type of the artifact that will be created upon importing. Use --show-importable-types to see what importable semantic types are available in the current deployment. [required] --input-path PATH Path to file or directory that should be imported. [required] --output-path ARTIFACT Path where output artifact should be written. [required] --input-format TEXT The format of the data to be imported. If not provided, data must be in the format expected by the semantic type provided via --type. --show-importable-types Show the semantic types that can be supplied to --type to import data into an artifact. --show-importable-formats Show formats that can be supplied to --input-format to import data into an artifact. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': Path './barcodes/manifest.txt' does not exist. Usage: qiime vsearch dereplicate-sequences [OPTIONS]

Dereplicate sequence data and create a feature table and feature representative sequences. Feature identifiers in the resulting artifacts will be the sha1 hash of the sequence defining each feature. If clustering of features into OTUs is desired, the resulting artifacts can be passed to the clusterfeatures* methods in this plugin.

Inputs: --i-sequences ARTIFACT SampleData[Sequences] | SampleData[SequencesWithQuality] | SampleData[JoinedSequencesWithQuality] The sequences to be dereplicated. [required] Parameters: --p-derep-prefix / --p-no-derep-prefix Merge sequences with identical prefixes. If a sequence is identical to the prefix of two or more longer sequences, it is clustered with the shortest of them. If they are equally long, it is clustered with the most abundant. [default: False] Outputs: --o-dereplicated-table ARTIFACT FeatureTable[Frequency] The table of dereplicated sequences. [required] --o-dereplicated-sequences ARTIFACT FeatureData[Sequence] The dereplicated sequences. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-sequences': 'sequences.qza' is not a valid filepath Usage: qiime vsearch cluster-features-de-novo [OPTIONS]

Given a feature table and the associated feature sequences, cluster the features based on user-specified percent identity threshold of their sequences. This is not a general-purpose de novo clustering method, but rather is intended to be used for clustering the results of quality- filtering/dereplication methods, such as DADA2, or for re-clustering a FeatureTable at a lower percent identity than it was originally clustered at. When a group of features in the input table are clustered into a single feature, the frequency of that single feature in a given sample is the sum of the frequencies of the features that were clustered in that sample. Feature identifiers and sequences will be inherited from the centroid feature of each cluster. See the vsearch documentation for details on how sequence clustering is performed.

Inputs: --i-sequences ARTIFACT FeatureData[Sequence] The sequences corresponding to the features in table. [required] --i-table ARTIFACT FeatureTable[Frequency] The feature table to be clustered. [required] Parameters: --p-perc-identity PROPORTION Range(0, 1, inclusive_start=False, inclusive_end=True) The percent identity at which clustering should be performed. This parameter maps to vsearch's --id parameter. [required] --p-threads INTEGER Range(0, 256, inclusive_end=True) The number of threads to use for computation. Passing 0 will launch one thread per CPU core. [default: 1] Outputs: --o-clustered-table ARTIFACT FeatureTable[Frequency] The table following clustering of features. [required] --o-clustered-sequences ARTIFACT FeatureData[Sequence] Sequences representing clustered features. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-sequences': 'rep-seqs_tmp.qza' is not a valid filepath (2/2) Invalid value for '--i-table': 'table_tmp.qza' is not a valid filepath rm: cannot remove 'table_tmp.qza': No such file or directory rm: cannot remove 'rep-seqs_tmp.qza': No such file or directory Usage: qiime demux summarize [OPTIONS]

Summarize counts per sample for all samples, and generate interactive positional quality plots based on n randomly selected sequences.

Inputs: --i-data ARTIFACT SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality] The demultiplexed sequences to be summarized. [required] Parameters: --p-n INTEGER The number of sequences that should be selected at random for quality score plots. The quality plots will present the average positional qualities across all of the sequences selected. If input sequences are paired end, plots will be generated for both forward and reverse reads for the same n sequences. [default: 10000] Outputs: --o-visualization VISUALIZATION [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-data': 'sequences.qza' is not a valid filepath There was an issue with loading the file ./sample-metadata.tsv as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): ./sample-metadata.tsv

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime feature-table tabulate-seqs [OPTIONS]

Generate tabular view of feature identifier to sequence mapping, including links to BLAST each sequence against the NCBI nt database.

Inputs: --i-data ARTIFACT FeatureData[Sequence | AlignedSequence] The feature sequences to be tabulated. [required] Outputs: --o-visualization VISUALIZATION [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-data': 'rep-seqs.qza' is not a valid filepath Usage: qiime feature-classifier classify-consensus-vsearch [OPTIONS]

Assign taxonomy to query sequences using VSEARCH. Performs VSEARCH global alignment between query and reference_reads, then assigns consensus taxonomy to each query sequence from among maxaccepts top hits, min_consensus of which share that taxonomic assignment. Unlike classify- consensus-blast, this method searches the entire reference database before choosing the top N hits, not the first N hits.

Inputs: --i-query ARTIFACT FeatureData[Sequence] Sequences to classify taxonomically. [required] --i-reference-reads ARTIFACT FeatureData[Sequence] reference sequences. [required] --i-reference-taxonomy ARTIFACT FeatureData[Taxonomy] reference taxonomy labels. [required] Parameters: --p-maxaccepts VALUE Int % Range(1, None) | Str % Choices('all') Maximum number of hits to keep for each query. Set to "all" to keep all hits > perc-identity similarity. Note that if strand=both, maxaccepts will keep N hits for each direction (if searches in the opposite direction yield results that exceed the minimum perc-identity). In those cases use maxhits to control the total number of hits returned. This option works in pair with maxrejects. The search process sorts target sequences by decreasing number of k-mers they have in common with the query sequence, using that information as a proxy for sequence similarity. After pairwise alignments, if the first target sequence passes the acceptation criteria, it is accepted as best hit and the search process stops for that query. If maxaccepts is set to a higher value, more hits are accepted. If maxaccepts and maxrejects are both set to "all", the complete database is searched. [default: 10] --p-perc-identity PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if percent identity to query is lower. [default: 0.8] --p-query-cov PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if query alignment coverage per high-scoring pair is lower. [default: 0.8] --p-strand TEXT Choices('both', 'plus') Align against reference sequences in forward ("plus") or both directions ("both"). [default: 'both'] --p-min-consensus NUMBER Range(0.5, 1.0, inclusive_start=False, inclusive_end=True) Minimum fraction of assignments must match top hit to be accepted as consensus assignment. [default: 0.51] --p-unassignable-label TEXT [default: 'Unassigned'] --p-search-exact / --p-no-search-exact Search for exact full-length matches to the query sequences. Only 100% exact matches are reported and this command is much faster than the default. If True, the perc-identity and query-cov settings are ignored. Note: query and reference reads must be trimmed to the exact same DNA locus (e.g., primer site) because only exact matches will be reported. [default: False] --p-top-hits-only / --p-no-top-hits-only Only the top hits between the query and reference sequence sets are reported. For each query, the top hit is the one presenting the highest percentage of identity. Multiple equally scored top hits will be used for consensus taxonomic assignment if maxaccepts is greater than 1. [default: False] --p-maxhits VALUE Int % Range(1, None) | Str % Choices('all') Maximum number of hits to show once the search is terminated. [default: 'all'] --p-maxrejects VALUE Int % Range(1, None) | Str % Choices('all') Maximum number of non-matching target sequences to consider before stopping the search. This option works in pair with maxaccepts (see maxaccepts description for details). [default: 'all'] --p-output-no-hits / --p-no-output-no-hits Report both matching and non-matching queries. WARNING: always use the default setting for this option unless if you know what you are doing! If you set this option to False, your sequences and feature table will need to be filtered to exclude unclassified sequences, otherwise you may run into errors downstream from missing feature IDs. [default: True] --p-weak-id PROPORTION Range(0.0, 1.0, inclusive_end=True) Show hits with percentage of identity of at least N, without terminating the search. A normal search stops as soon as enough hits are found (as defined by maxaccepts, maxrejects, and perc-identity). As weak-id reports weak hits that are not deduced from maxaccepts, high perc-identity values can be used, hence preserving both speed and sensitivity. Logically, weak-id must be smaller than the value indicated by perc-identity, otherwise this option will be ignored. [default: 0.0] --p-threads INTEGER Number of threads to use for job parallelization. Range(1, None) [default: 1] Outputs: --o-classification ARTIFACT FeatureData[Taxonomy] The resulting taxonomy classifications. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/3) Invalid value for '--i-query': 'rep-seqs.qza' is not a valid filepath (2/3) Invalid value for '--i-reference-reads': './silva_132_99_16S_sequence.qza' is not a valid filepath (3/3) Invalid value for '--i-reference-taxonomy': './silva_132_99_16S_taxonomy.qza' is not a valid filepath There was an issue with loading the file taxonomy.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): taxonomy.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

There was an issue with loading the file ./sample-metadata.tsv as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): ./sample-metadata.tsv

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime taxa filter-table [OPTIONS]

This method filters features from a table based on their taxonomic annotations. Features can be retained in the resulting table by specifying one or more include search terms, and can be filtered out of the resulting table by specifying one or more exclude search terms. If both include and exclude are provided, the inclusion critera will be applied before the exclusion critera. Either include or exclude terms (or both) must be provided. Any samples that have a total frequency of zero after filtering will be removed from the resulting table.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be filtered. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations for features that are not present in the feature table will be ignored. [required] Parameters: --p-include TEXT One or more search terms that indicate which taxa should be included in the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, all taxa will be included. [optional] --p-exclude TEXT One or more search terms that indicate which taxa should be excluded from the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, no taxa will be excluded. [optional] --p-query-delimiter TEXT The string used to delimit multiple search terms provided to include or exclude. This parameter should only need to be modified if the default delimiter (a comma) is used in the provided taxonomic annotations. [default: ','] --p-mode TEXT Choices('exact', 'contains') Mode for determining if a search term matches a taxonomic annotation. "contains" requires that the annotation has the term as a substring; "exact" requires that the annotation is a perfect match to a search term. [default: 'contains'] Outputs: --o-filtered-table ARTIFACT FeatureTable[Frequency] The taxonomy-filtered feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file ./sample-metadata.tsv as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): ./sample-metadata.tsv

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level1.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level1.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level1.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level1.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS]

Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level1.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level1.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level1.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level1.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level1.biom' does not exist. cat: feature-table_absfreq_level1.tsv: No such file or directory cat: feature-table_absfreq_level1.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level2.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level2.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level2.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level2.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS]

Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level2.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level2.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level2.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level2.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level2.biom' does not exist. cat: feature-table_absfreq_level2.tsv: No such file or directory cat: feature-table_absfreq_level2.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level3.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level3.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level3.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level3.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS]

Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level3.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level3.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level3.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level3.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level3.biom' does not exist. cat: feature-table_absfreq_level3.tsv: No such file or directory cat: feature-table_absfreq_level3.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level4.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level4.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level4.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level4.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS]

Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level4.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level4.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level4.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level4.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level4.biom' does not exist. cat: feature-table_absfreq_level4.tsv: No such file or directory cat: feature-table_absfreq_level4.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level5.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level5.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level5.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level5.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS]

Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level5.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level5.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level5.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level5.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level5.biom' does not exist. cat: feature-table_absfreq_level5.tsv: No such file or directory cat: feature-table_absfreq_level5.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level6.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level6.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level6.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level6.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS]

Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level6.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level6.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level6.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level6.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level6.biom' does not exist. cat: feature-table_absfreq_level6.tsv: No such file or directory cat: feature-table_absfreq_level6.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided featur

[MaestSi]

Are you sure you are uploading the errors occurred during this last test? In your command line I see a full path: /home/qiime2/barcodes while the error reports a relative path:

(1/1) Invalid value for '--input-path': Path './barcodes/manifest.txt' does
  not exist.

Moreover, are you sure you have writing permissions and the Silva files in /home directory (instead of /home/qiime2 as before)? This time I saw you specified: /home/sample-metadata.tsv /home/silva_132_99_16S_sequence.qza /home/silva_132_99_16S_taxonomy.qza I would also need to know which files were produced by the pipeline, in order to understand where it stopped. Simone

[dinavb]

I tried: nohup ./MetONTIIME/MetONTIIME.sh /home/qiime2/barcodes /home/qiime2/sample-metadata.tsv /home/qiime2/silva_132_99_16S_sequence.qza /home/qiime2/silva_132_99_16S_taxonomy.qza 5 Vsearch 3 0.8 0.85 nohup: ignoring input and appending output to 'nohup.out' I attach the files

On Tue, Dec 1, 2020 at 5:38 PM Simone Maestri notifications@github.com wrote:

Are you sure you are uploading the errors occurred during this last test? In your command line I see a full path: /home/qiime2/barcodes while the error reports a relative path:

(1/1) Invalid value for '--input-path': Path './barcodes/manifest.txt' does not exist.

Moreover, are you sure you have writing permissions and the Silva files in /home directory (instead of /home/qiime2 as before)? This time I saw you specified: /home/sample-metadata.tsv /home/silva_132_99_16S_sequence.qza /home/silva_132_99_16S_taxonomy.qza Simone

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/MaestSi/MetONTIIME/issues/20#issuecomment-736632091, or unsubscribe https://github.com/notifications/unsubscribe-auth/AR34USVXO6DDHXSXU36E6TTSSUEWVANCNFSM4UAYZG7Q .

sample-id absolute-filepath barcode04 /home/qiime2/barcodes/barcode04.fastq.gz barcode07 /home/qiime2/barcodes/barcode07.fastq.gz barcode02 /home/qiime2/barcodes/barcode02.fastq.gz barcode06 /home/qiime2/barcodes/barcode06.fastq.gz barcode05 /home/qiime2/barcodes/barcode05.fastq.gz

Imported /home/qiime2/barcodes/manifest.txt as SingleEndFastqManifestPhred33V2 to sequences.qza Plugin error from vsearch:

Command '['vsearch', '--derep_fulllength', '/tmp/q2-QIIME1DemuxDirFmt-wzbq9gn4/seqs.fna', '--output', '/tmp/q2-DNAFASTAFormat-mvqep2qx', '--relabel_sha1', '--relabel_keep', '--uc', '/tmp/tmpym81enps', '--qmask', 'none', '--xsize', '--minseqlength', '1', '--fasta_width', '0']' died with <Signals.SIGKILL: 9>.

Debug info has been saved to /tmp/qiime2-q2cli-err-xaybqip2.log Usage: qiime vsearch cluster-features-de-novo [OPTIONS]

Given a feature table and the associated feature sequences, cluster the features based on user-specified percent identity threshold of their sequences. This is not a general-purpose de novo clustering method, but rather is intended to be used for clustering the results of quality- filtering/dereplication methods, such as DADA2, or for re-clustering a FeatureTable at a lower percent identity than it was originally clustered at. When a group of features in the input table are clustered into a single feature, the frequency of that single feature in a given sample is the sum of the frequencies of the features that were clustered in that sample. Feature identifiers and sequences will be inherited from the centroid feature of each cluster. See the vsearch documentation for details on how sequence clustering is performed.

Inputs: --i-sequences ARTIFACT FeatureData[Sequence] The sequences corresponding to the features in table. [required] --i-table ARTIFACT FeatureTable[Frequency] The feature table to be clustered. [required] Parameters: --p-perc-identity PROPORTION Range(0, 1, inclusive_start=False, inclusive_end=True) The percent identity at which clustering should be performed. This parameter maps to vsearch's --id parameter. [required] --p-threads INTEGER Range(0, 256, inclusive_end=True) The number of threads to use for computation. Passing 0 will launch one thread per CPU core. [default: 1] Outputs: --o-clustered-table ARTIFACT FeatureTable[Frequency] The table following clustering of features. [required] --o-clustered-sequences ARTIFACT FeatureData[Sequence] Sequences representing clustered features. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-sequences': 'rep-seqs_tmp.qza' is not a valid filepath (2/2) Invalid value for '--i-table': 'table_tmp.qza' is not a valid filepath rm: cannot remove 'table_tmp.qza': No such file or directory rm: cannot remove 'rep-seqs_tmp.qza': No such file or directory Saved Visualization to: demux_summary.qzv Usage: qiime feature-table summarize [OPTIONS]

Generate visual and tabular summaries of a feature table.

Inputs: --i-table ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence] The feature table to be summarized. [required] Parameters: --m-sample-metadata-file METADATA... (multiple The sample metadata. arguments will
be merged) [optional] Outputs: --o-visualization VISUALIZATION [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-table': 'table.qza' is not a valid filepath Usage: qiime feature-table tabulate-seqs [OPTIONS]

Generate tabular view of feature identifier to sequence mapping, including links to BLAST each sequence against the NCBI nt database.

Inputs: --i-data ARTIFACT FeatureData[Sequence | AlignedSequence] The feature sequences to be tabulated. [required] Outputs: --o-visualization VISUALIZATION [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-data': 'rep-seqs.qza' is not a valid filepath Usage: qiime feature-classifier classify-consensus-vsearch [OPTIONS]

Assign taxonomy to query sequences using VSEARCH. Performs VSEARCH global alignment between query and reference_reads, then assigns consensus taxonomy to each query sequence from among maxaccepts top hits, min_consensus of which share that taxonomic assignment. Unlike classify- consensus-blast, this method searches the entire reference database before choosing the top N hits, not the first N hits.

Inputs: --i-query ARTIFACT FeatureData[Sequence] Sequences to classify taxonomically. [required] --i-reference-reads ARTIFACT FeatureData[Sequence] reference sequences. [required] --i-reference-taxonomy ARTIFACT FeatureData[Taxonomy] reference taxonomy labels. [required] Parameters: --p-maxaccepts VALUE Int % Range(1, None) | Str % Choices('all') Maximum number of hits to keep for each query. Set to "all" to keep all hits > perc-identity similarity. Note that if strand=both, maxaccepts will keep N hits for each direction (if searches in the opposite direction yield results that exceed the minimum perc-identity). In those cases use maxhits to control the total number of hits returned. This option works in pair with maxrejects. The search process sorts target sequences by decreasing number of k-mers they have in common with the query sequence, using that information as a proxy for sequence similarity. After pairwise alignments, if the first target sequence passes the acceptation criteria, it is accepted as best hit and the search process stops for that query. If maxaccepts is set to a higher value, more hits are accepted. If maxaccepts and maxrejects are both set to "all", the complete database is searched. [default: 10] --p-perc-identity PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if percent identity to query is lower. [default: 0.8] --p-query-cov PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if query alignment coverage per high-scoring pair is lower. [default: 0.8] --p-strand TEXT Choices('both', 'plus') Align against reference sequences in forward ("plus") or both directions ("both"). [default: 'both'] --p-min-consensus NUMBER Range(0.5, 1.0, inclusive_start=False, inclusive_end=True) Minimum fraction of assignments must match top hit to be accepted as consensus assignment. [default: 0.51] --p-unassignable-label TEXT [default: 'Unassigned'] --p-search-exact / --p-no-search-exact Search for exact full-length matches to the query sequences. Only 100% exact matches are reported and this command is much faster than the default. If True, the perc-identity and query-cov settings are ignored. Note: query and reference reads must be trimmed to the exact same DNA locus (e.g., primer site) because only exact matches will be reported. [default: False] --p-top-hits-only / --p-no-top-hits-only Only the top hits between the query and reference sequence sets are reported. For each query, the top hit is the one presenting the highest percentage of identity. Multiple equally scored top hits will be used for consensus taxonomic assignment if maxaccepts is greater than 1. [default: False] --p-maxhits VALUE Int % Range(1, None) | Str % Choices('all') Maximum number of hits to show once the search is terminated. [default: 'all'] --p-maxrejects VALUE Int % Range(1, None) | Str % Choices('all') Maximum number of non-matching target sequences to consider before stopping the search. This option works in pair with maxaccepts (see maxaccepts description for details). [default: 'all'] --p-output-no-hits / --p-no-output-no-hits Report both matching and non-matching queries. WARNING: always use the default setting for this option unless if you know what you are doing! If you set this option to False, your sequences and feature table will need to be filtered to exclude unclassified sequences, otherwise you may run into errors downstream from missing feature IDs. [default: True] --p-weak-id PROPORTION Range(0.0, 1.0, inclusive_end=True) Show hits with percentage of identity of at least N, without terminating the search. A normal search stops as soon as enough hits are found (as defined by maxaccepts, maxrejects, and perc-identity). As weak-id reports weak hits that are not deduced from maxaccepts, high perc-identity values can be used, hence preserving both speed and sensitivity. Logically, weak-id must be smaller than the value indicated by perc-identity, otherwise this option will be ignored. [default: 0.0] --p-threads INTEGER Number of threads to use for job parallelization. Range(1, None) [default: 1] Outputs: --o-classification ARTIFACT FeatureData[Taxonomy] The resulting taxonomy classifications. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-query': 'rep-seqs.qza' is not a valid filepath There was an issue with loading the file taxonomy.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): taxonomy.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime taxa barplot [OPTIONS]

This visualizer produces an interactive barplot visualization of taxonomies. Interactive features include multi-level sorting, plot recoloring, sample relabeling, and SVG figure export.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to visualize at various taxonomic levels. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --m-metadata-file METADATA... (multiple The sample metadata. arguments will be
merged) [required] Outputs: --o-visualization VISUALIZATION [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath Usage: qiime taxa filter-table [OPTIONS]

This method filters features from a table based on their taxonomic annotations. Features can be retained in the resulting table by specifying one or more include search terms, and can be filtered out of the resulting table by specifying one or more exclude search terms. If both include and exclude are provided, the inclusion critera will be applied before the exclusion critera. Either include or exclude terms (or both) must be provided. Any samples that have a total frequency of zero after filtering will be removed from the resulting table.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be filtered. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations for features that are not present in the feature table will be ignored. [required] Parameters: --p-include TEXT One or more search terms that indicate which taxa should be included in the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, all taxa will be included. [optional] --p-exclude TEXT One or more search terms that indicate which taxa should be excluded from the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, no taxa will be excluded. [optional] --p-query-delimiter TEXT The string used to delimit multiple search terms provided to include or exclude. This parameter should only need to be modified if the default delimiter (a comma) is used in the provided taxonomic annotations. [default: ','] --p-mode TEXT Choices('exact', 'contains') Mode for determining if a search term matches a taxonomic annotation. "contains" requires that the annotation has the term as a substring; "exact" requires that the annotation is a perfect match to a search term. [default: 'contains'] Outputs: --o-filtered-table ARTIFACT FeatureTable[Frequency] The taxonomy-filtered feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath Usage: qiime taxa barplot [OPTIONS]

This visualizer produces an interactive barplot visualization of taxonomies. Interactive features include multi-level sorting, plot recoloring, sample relabeling, and SVG figure export.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to visualize at various taxonomic levels. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --m-metadata-file METADATA... (multiple The sample metadata. arguments will be
merged) [required] Outputs: --o-visualization VISUALIZATION [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table-no-Unassigned.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level1.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level1.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level1.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level1.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS]

Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level1.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level1.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level1.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level1.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level1.biom' does not exist. cat: feature-table_absfreq_level1.tsv: No such file or directory cat: feature-table_absfreq_level1.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level2.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level2.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level2.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level2.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS]

Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level2.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level2.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level2.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level2.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level2.biom' does not exist. cat: feature-table_absfreq_level2.tsv: No such file or directory cat: feature-table_absfreq_level2.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level3.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level3.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level3.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level3.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS]

Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level3.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level3.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level3.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level3.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level3.biom' does not exist. cat: feature-table_absfreq_level3.tsv: No such file or directory cat: feature-table_absfreq_level3.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level4.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level4.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level4.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level4.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS]

Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level4.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level4.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level4.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level4.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level4.biom' does not exist. cat: feature-table_absfreq_level4.tsv: No such file or directory cat: feature-table_absfreq_level4.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level5.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level5.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level5.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level5.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS]

Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level5.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level5.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level5.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level5.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level5.biom' does not exist. cat: feature-table_absfreq_level5.tsv: No such file or directory cat: feature-table_absfreq_level5.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level6.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level6.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level6.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level6.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS]

Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level6.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level6.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level6.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level6.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level6.biom' does not exist. cat: feature-table_absfreq_level6.tsv: No such file or directory cat: feature-table_absfreq_level6.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level7.qza as metadata:

Meta

[MaestSi]

Hi, this is the error:

Command '['vsearch', '--derep_fulllength', '/tmp/q2-QIIME1DemuxDirFmt-wzbq9gn4/seqs.fna', '--output', '/tmp/q2-DNAFASTAFormat-mvqep2qx', '--relabel_sha1', '--relabel_keep', '--uc', '/tmp/tmpym81enps', '--qmask', 'none', '--xsize', '--minseqlength', '1', '--fasta_width', '0']' died with <Signals.SIGKILL: 9>.

Based on this post it looks like your pc may be running out of memory. How much RAM memory does your pc have? Are you running inside a virtual machine? If you want to confirm the issue is due to the memory, just try running the pipeline on a small set of reads. For example try the following and let me know if it produces the expected files in the/home/qiime2/subsampling_analysis folder:

source activate MetONTIIME_env
cd /home/qiime2
mkdir subsampling_analysis
for fq in $(find /home/qiime2/barcodes | grep "\.fastq.gz"); do
  sn=$(basename $fq);
  seqtk sample $fq 100 | gzip > subsampling/$sn;
done

nohup /home/qiime2/MetONTIIME/MetONTIIME.sh /home/qiime2/subsampling_analysis/
/home/qiime2/subsampling_analysis/sample-metadata.tsv /home/qiime2/silva_132_99_16S_sequence.qza
/home/qiime2/silva_132_99_16S_taxonomy.qza 5 Vsearch 3 0.8 0.85 &

Simone

[dinavb]

Hi Simone, yes, we run in virtual machine. We enlarged the RAM and run again. I attach the files received now.

On Wed, Dec 2, 2020 at 3:33 PM Simone Maestri notifications@github.com wrote:

Hi, this is the error:

Command '['vsearch', '--derep_fulllength', '/tmp/q2-QIIME1DemuxDirFmt-wzbq9gn4/seqs.fna', '--output', '/tmp/q2-DNAFASTAFormat-mvqep2qx', '--relabel_sha1', '--relabel_keep', '--uc', '/tmp/tmpym81enps', '--qmask', 'none', '--xsize', '--minseqlength', '1', '--fasta_width', '0']' died with <Signals.SIGKILL: 9>.

Based on this post https://forum.qiime2.org/t/error-while-dereplicating-sequences/10907 it looks like your pc may be running out of memory. How much RAM memory does your pc have? Are you running inside a virtual machine? If you want to confirm the issue is due to the memory, just try running the pipeline on a small set of reads. For example try the following and let me know if it produces the expected files in the /home/qiime2/subsampling_analysis folder:

source activate MetONTIIME_env cd /home/qiime2 mkdir subsampling_analysis for fq in $(find /home/qiime2/barcodes | grep ".fastq.gz"); do sn=$(basename $fq); seqtk sample $fq 100 | gzip > subsampling/$sn; done

nohup /home/qiime2/MetONTIIME/MetONTIIME.sh /home/qiime2/subsampling_analysis/ /home/qiime2/subsampling_analysis/sample-metadata.tsv /home/qiime2/silva_132_99_16S_sequence.qza /home/qiime2/silva_132_99_16S_taxonomy.qza 5 Vsearch 3 0.8 0.85 &

Simone

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/MaestSi/MetONTIIME/issues/20#issuecomment-737232624, or unsubscribe https://github.com/notifications/unsubscribe-auth/AR34USUZLZDY7HUY3J5FS7DSSY63NANCNFSM4UAYZG7Q .

Imported /home/qiime2/barcodes/manifest.txt as SingleEndFastqManifestPhred33V2 to sequences.qza Saved FeatureTable[Frequency] to: table_tmp.qza Saved FeatureData[Sequence] to: rep-seqs_tmp.qza Plugin error from vsearch:

Command '['vsearch', '--cluster_size', '/tmp/tmpkf5uftbj', '--id', '1.0', '--centroids', '/tmp/q2-DNAFASTAFormat-xenaluiw', '--uc', '/tmp/tmpxzm3ydfz', '--qmask', 'none', '--xsize', '--threads', '5', '--minseqlength', '1', '--fasta_width', '0']' returned non-zero exit status 1.

Debug info has been saved to /tmp/qiime2-q2cli-err-mdpernji.log Saved Visualization to: demux_summary.qzv Usage: qiime feature-table summarize [OPTIONS]

Generate visual and tabular summaries of a feature table.

Inputs: --i-table ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence] The feature table to be summarized. [required] Parameters: --m-sample-metadata-file METADATA... (multiple The sample metadata. arguments will
be merged) [optional] Outputs: --o-visualization VISUALIZATION [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-table': 'table.qza' is not a valid filepath Usage: qiime feature-table tabulate-seqs [OPTIONS]

Generate tabular view of feature identifier to sequence mapping, including links to BLAST each sequence against the NCBI nt database.

Inputs: --i-data ARTIFACT FeatureData[Sequence | AlignedSequence] The feature sequences to be tabulated. [required] Outputs: --o-visualization VISUALIZATION [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-data': 'rep-seqs.qza' is not a valid filepath Usage: qiime feature-classifier classify-consensus-vsearch [OPTIONS]

Assign taxonomy to query sequences using VSEARCH. Performs VSEARCH global alignment between query and reference_reads, then assigns consensus taxonomy to each query sequence from among maxaccepts top hits, min_consensus of which share that taxonomic assignment. Unlike classify- consensus-blast, this method searches the entire reference database before choosing the top N hits, not the first N hits.

Inputs: --i-query ARTIFACT FeatureData[Sequence] Sequences to classify taxonomically. [required] --i-reference-reads ARTIFACT FeatureData[Sequence] reference sequences. [required] --i-reference-taxonomy ARTIFACT FeatureData[Taxonomy] reference taxonomy labels. [required] Parameters: --p-maxaccepts VALUE Int % Range(1, None) | Str % Choices('all') Maximum number of hits to keep for each query. Set to "all" to keep all hits > perc-identity similarity. Note that if strand=both, maxaccepts will keep N hits for each direction (if searches in the opposite direction yield results that exceed the minimum perc-identity). In those cases use maxhits to control the total number of hits returned. This option works in pair with maxrejects. The search process sorts target sequences by decreasing number of k-mers they have in common with the query sequence, using that information as a proxy for sequence similarity. After pairwise alignments, if the first target sequence passes the acceptation criteria, it is accepted as best hit and the search process stops for that query. If maxaccepts is set to a higher value, more hits are accepted. If maxaccepts and maxrejects are both set to "all", the complete database is searched. [default: 10] --p-perc-identity PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if percent identity to query is lower. [default: 0.8] --p-query-cov PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if query alignment coverage per high-scoring pair is lower. [default: 0.8] --p-strand TEXT Choices('both', 'plus') Align against reference sequences in forward ("plus") or both directions ("both"). [default: 'both'] --p-min-consensus NUMBER Range(0.5, 1.0, inclusive_start=False, inclusive_end=True) Minimum fraction of assignments must match top hit to be accepted as consensus assignment. [default: 0.51] --p-unassignable-label TEXT [default: 'Unassigned'] --p-search-exact / --p-no-search-exact Search for exact full-length matches to the query sequences. Only 100% exact matches are reported and this command is much faster than the default. If True, the perc-identity and query-cov settings are ignored. Note: query and reference reads must be trimmed to the exact same DNA locus (e.g., primer site) because only exact matches will be reported. [default: False] --p-top-hits-only / --p-no-top-hits-only Only the top hits between the query and reference sequence sets are reported. For each query, the top hit is the one presenting the highest percentage of identity. Multiple equally scored top hits will be used for consensus taxonomic assignment if maxaccepts is greater than 1. [default: False] --p-maxhits VALUE Int % Range(1, None) | Str % Choices('all') Maximum number of hits to show once the search is terminated. [default: 'all'] --p-maxrejects VALUE Int % Range(1, None) | Str % Choices('all') Maximum number of non-matching target sequences to consider before stopping the search. This option works in pair with maxaccepts (see maxaccepts description for details). [default: 'all'] --p-output-no-hits / --p-no-output-no-hits Report both matching and non-matching queries. WARNING: always use the default setting for this option unless if you know what you are doing! If you set this option to False, your sequences and feature table will need to be filtered to exclude unclassified sequences, otherwise you may run into errors downstream from missing feature IDs. [default: True] --p-weak-id PROPORTION Range(0.0, 1.0, inclusive_end=True) Show hits with percentage of identity of at least N, without terminating the search. A normal search stops as soon as enough hits are found (as defined by maxaccepts, maxrejects, and perc-identity). As weak-id reports weak hits that are not deduced from maxaccepts, high perc-identity values can be used, hence preserving both speed and sensitivity. Logically, weak-id must be smaller than the value indicated by perc-identity, otherwise this option will be ignored. [default: 0.0] --p-threads INTEGER Number of threads to use for job parallelization. Range(1, None) [default: 1] Outputs: --o-classification ARTIFACT FeatureData[Taxonomy] The resulting taxonomy classifications. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-query': 'rep-seqs.qza' is not a valid filepath There was an issue with loading the file taxonomy.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): taxonomy.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime taxa barplot [OPTIONS]

This visualizer produces an interactive barplot visualization of taxonomies. Interactive features include multi-level sorting, plot recoloring, sample relabeling, and SVG figure export.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to visualize at various taxonomic levels. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --m-metadata-file METADATA... (multiple The sample metadata. arguments will be
merged) [required] Outputs: --o-visualization VISUALIZATION [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath Usage: qiime taxa filter-table [OPTIONS]

This method filters features from a table based on their taxonomic annotations. Features can be retained in the resulting table by specifying one or more include search terms, and can be filtered out of the resulting table by specifying one or more exclude search terms. If both include and exclude are provided, the inclusion critera will be applied before the exclusion critera. Either include or exclude terms (or both) must be provided. Any samples that have a total frequency of zero after filtering will be removed from the resulting table.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be filtered. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations for features that are not present in the feature table will be ignored. [required] Parameters: --p-include TEXT One or more search terms that indicate which taxa should be included in the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, all taxa will be included. [optional] --p-exclude TEXT One or more search terms that indicate which taxa should be excluded from the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, no taxa will be excluded. [optional] --p-query-delimiter TEXT The string used to delimit multiple search terms provided to include or exclude. This parameter should only need to be modified if the default delimiter (a comma) is used in the provided taxonomic annotations. [default: ','] --p-mode TEXT Choices('exact', 'contains') Mode for determining if a search term matches a taxonomic annotation. "contains" requires that the annotation has the term as a substring; "exact" requires that the annotation is a perfect match to a search term. [default: 'contains'] Outputs: --o-filtered-table ARTIFACT FeatureTable[Frequency] The taxonomy-filtered feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath Usage: qiime taxa barplot [OPTIONS]

This visualizer produces an interactive barplot visualization of taxonomies. Interactive features include multi-level sorting, plot recoloring, sample relabeling, and SVG figure export.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to visualize at various taxonomic levels. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --m-metadata-file METADATA... (multiple The sample metadata. arguments will be
merged) [required] Outputs: --o-visualization VISUALIZATION [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table-no-Unassigned.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level1.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level1.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level1.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level1.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS]

Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level1.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level1.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level1.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level1.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level1.biom' does not exist. cat: feature-table_absfreq_level1.tsv: No such file or directory cat: feature-table_absfreq_level1.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level2.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level2.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level2.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level2.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS]

Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level2.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level2.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level2.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level2.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level2.biom' does not exist. cat: feature-table_absfreq_level2.tsv: No such file or directory cat: feature-table_absfreq_level2.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level3.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level3.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level3.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level3.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS]

Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level3.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level3.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level3.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level3.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level3.biom' does not exist. cat: feature-table_absfreq_level3.tsv: No such file or directory cat: feature-table_absfreq_level3.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level4.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level4.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level4.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level4.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS]

Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level4.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level4.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level4.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level4.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level4.biom' does not exist. cat: feature-table_absfreq_level4.tsv: No such file or directory cat: feature-table_absfreq_level4.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level5.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level5.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level5.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level5.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS]

Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level5.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level5.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level5.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level5.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level5.biom' does not exist. cat: feature-table_absfreq_level5.tsv: No such file or directory cat: feature-table_absfreq_level5.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level6.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level6.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level6.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level6.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS]

Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level6.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level6.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level6.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level6.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level6.biom' does not exist. cat: feature-table_absfreq_level6.tsv: No such file or directory cat: feature-table_absfreq_level6.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS]

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

              There were some problems with the command:                  

(1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level7.qza as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level7.qza

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format

Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level7.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help.

Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level7.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS]

Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample.

Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:       

[MaestSi]

It seems it is a RAM issue, the error looks like exactly the same as before. Have you tried subsampling the dataset as suggested? P.s.: I don't think you are attaching any files, you are just reporting the full standard output/error written in the nohup.out file. Readability could be increased if you could either upload the nohup.out file (after renaming to nohup.out.txt, but remind to delete it after each test, because the new output is appended at the end of the file) or just provide the first error. Thanks

[dinavb]

Attached is the output for subsampling.. the RAM is 6. The maximum RAM we have at the moment is 8. Should it be enough for full analysis? What are the other hardware requirements if we need to analyze a full run of 24 samples?

On Thu, Dec 10, 2020 at 10:07 AM Simone Maestri notifications@github.com wrote:

It seems it is a RAM issue, the error looks like exactly the same as before. Have you tried subsampling the dataset as suggested?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/MaestSi/MetONTIIME/issues/20#issuecomment-742351114, or unsubscribe https://github.com/notifications/unsubscribe-auth/AR34USW3TIRVVIGXNFVZSLTSUB6S5ANCNFSM4UAYZG7Q .

Imported /home/qiime2/subsampling//manifest.txt as SingleEndFastqManifestPhred33V2 to sequences.qza Saved FeatureTable[Frequency] to: table_tmp.qza Saved FeatureData[Sequence] to: rep-seqs_tmp.qza Usage: qiime vsearch cluster-features-de-novo [OPTIONS]

Given a feature table and the associated feature sequences, cluster the features based on user-specified percent identity threshold of their sequences. This is not a general-purpose de novo clustering method, but rather is intended to be used for clustering the results of quality- filtering/dereplication methods, such as DADA2, or for re-clustering a FeatureTable at a lower percent identity than it was originally clustered at. When a group of features in the input table are clustered into a single feature, the frequency of that single feature in a given sample is the sum of the frequencies of the features that were clustered in that sample. Feature identifiers and sequences will be inherited from the centroid feature of each cluster. See the vsearch documentation for details on how sequence clustering is performed.

Inputs: --i-sequences ARTIFACT FeatureData[Sequence] The sequences corresponding to the features in table. [required] --i-table ARTIFACT FeatureTable[Frequency] The feature table to be clustered. [required] Parameters: --p-perc-identity PROPORTION Range(0, 1, inclusive_start=False, inclusive_end=True) The percent identity at which clustering should be performed. This parameter maps to vsearch's --id parameter. [required] --p-threads INTEGER Range(0, 256, inclusive_end=True) The number of threads to use for computation. Passing 0 will launch one thread per CPU core. [default: 1] Outputs: --o-clustered-table ARTIFACT FeatureTable[Frequency] The table following clustering of features. [required] --o-clustered-sequences ARTIFACT FeatureData[Sequence] Sequences representing clustered features. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit.

                There was a problem with the command:                     

(1/1) Invalid value for '--p-threads': received

as an argument, which is incompatible with parameter type: Int % Range(0, 256, inclusive_end=True) Imported /home/qiime2/subsampling//manifest.txt as SingleEndFastqManifestPhred33V2 to sequences.qza Saved FeatureTable[Frequency] to: table_tmp.qza Saved FeatureData[Sequence] to: rep-seqs_tmp.qza Usage: qiime vsearch cluster-features-de-novo [OPTIONS] Given a feature table and the associated feature sequences, cluster the features based on user-specified percent identity threshold of their sequences. This is not a general-purpose de novo clustering method, but rather is intended to be used for clustering the results of quality- filtering/dereplication methods, such as DADA2, or for re-clustering a FeatureTable at a lower percent identity than it was originally clustered at. When a group of features in the input table are clustered into a single feature, the frequency of that single feature in a given sample is the sum of the frequencies of the features that were clustered in that sample. Feature identifiers and sequences will be inherited from the centroid feature of each cluster. See the vsearch documentation for details on how sequence clustering is performed. Inputs: --i-sequences ARTIFACT FeatureData[Sequence] The sequences corresponding to the features in table. [required] --i-table ARTIFACT FeatureTable[Frequency] The feature table to be clustered. [required] Parameters: --p-perc-identity PROPORTION Range(0, 1, inclusive_start=False, inclusive_end=True) The percent identity at which clustering should be performed. This parameter maps to vsearch's --id parameter. [required] --p-threads INTEGER Range(0, 256, inclusive_end=True) The number of threads to use for computation. Passing 0 will launch one thread per CPU core. [default: 1] Outputs: --o-clustered-table ARTIFACT FeatureTable[Frequency] The table following clustering of features. [required] --o-clustered-sequences ARTIFACT FeatureData[Sequence] Sequences representing clustered features. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--p-threads': received as an argument, which is incompatible with parameter type: Int % Range(0, 256, inclusive_end=True) Saved Visualization to: demux_summary.qzv Usage: qiime feature-table summarize [OPTIONS] Generate visual and tabular summaries of a feature table. Inputs: --i-table ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence] The feature table to be summarized. [required] Parameters: --m-sample-metadata-file METADATA... (multiple The sample metadata. arguments will be merged) [optional] Outputs: --o-visualization VISUALIZATION [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--i-table': 'table.qza' is not a valid filepath Usage: qiime feature-table tabulate-seqs [OPTIONS] Generate tabular view of feature identifier to sequence mapping, including links to BLAST each sequence against the NCBI nt database. Inputs: --i-data ARTIFACT FeatureData[Sequence | AlignedSequence] The feature sequences to be tabulated. [required] Outputs: --o-visualization VISUALIZATION [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--i-data': 'rep-seqs.qza' is not a valid filepath Classifier 5 is not supported (choose between Blast and Vsearch); running default classifier Blast Usage: qiime feature-classifier classify-consensus-blast [OPTIONS] Assign taxonomy to query sequences using BLAST+. Performs BLAST+ local alignment between query and reference_reads, then assigns consensus taxonomy to each query sequence from among maxaccepts hits, min_consensus of which share that taxonomic assignment. Note that maxaccepts selects the first N hits with > perc_identity similarity to query, not the top N matches. For top N hits, use classify-consensus-vsearch. Inputs: --i-query ARTIFACT FeatureData[Sequence] Sequences to classify taxonomically. [required] --i-reference-reads ARTIFACT FeatureData[Sequence] reference sequences. [required] --i-reference-taxonomy ARTIFACT FeatureData[Taxonomy] reference taxonomy labels. [required] Parameters: --p-maxaccepts INTEGER Maximum number of hits to keep for each query. Must Range(1, None) be in range [1, infinity]. BLAST will choose the first N hits in the reference database that exceed perc-identity similarity to query. [default: 10] --p-perc-identity PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if percent identity to query is lower. Must be in range [0.0, 1.0]. [default: 0.8] --p-query-cov PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if query alignment coverage per high-scoring pair is lower. Note: this uses blastn's qcov_hsp_perc parameter, and may not behave identically to the query-cov parameter used by classify-consensus-vsearch. Must be in range [0.0, 1.0]. [default: 0.8] --p-strand TEXT Choices('both', 'plus', 'minus') Align against reference sequences in forward ("plus"), reverse ("minus"), or both directions ("both"). [default: 'both'] --p-evalue NUMBER BLAST expectation value (E) threshold for saving hits. [default: 0.001] --p-min-consensus NUMBER Range(0.5, 1.0, inclusive_start=False, inclusive_end=True) Minimum fraction of assignments must match top hit to be accepted as consensus assignment. Must be in range (0.5, 1.0]. [default: 0.51] --p-unassignable-label TEXT [default: 'Unassigned'] Outputs: --o-classification ARTIFACT FeatureData[Taxonomy] Taxonomy classifications of query sequences. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There were some problems with the command: (1/3) Invalid value for '--i-query': 'rep-seqs.qza' is not a valid filepath (2/3) Invalid value for '--i-reference-taxonomy': '/home/qiime2' is not a QIIME 2 Artifact (.qza) (3/3) Invalid value for '--p-maxaccepts': received as an argument, which is incompatible with parameter type: Int % Range(1, None) There was an issue with loading the file taxonomy.qza as metadata: Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): taxonomy.qza There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/ Usage: qiime taxa barplot [OPTIONS] This visualizer produces an interactive barplot visualization of taxonomies. Interactive features include multi-level sorting, plot recoloring, sample relabeling, and SVG figure export. Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to visualize at various taxonomic levels. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --m-metadata-file METADATA... (multiple The sample metadata. arguments will be merged) [required] Outputs: --o-visualization VISUALIZATION [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There were some problems with the command: (1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath Usage: qiime taxa filter-table [OPTIONS] This method filters features from a table based on their taxonomic annotations. Features can be retained in the resulting table by specifying one or more include search terms, and can be filtered out of the resulting table by specifying one or more exclude search terms. If both include and exclude are provided, the inclusion critera will be applied before the exclusion critera. Either include or exclude terms (or both) must be provided. Any samples that have a total frequency of zero after filtering will be removed from the resulting table. Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be filtered. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations for features that are not present in the feature table will be ignored. [required] Parameters: --p-include TEXT One or more search terms that indicate which taxa should be included in the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, all taxa will be included. [optional] --p-exclude TEXT One or more search terms that indicate which taxa should be excluded from the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, no taxa will be excluded. [optional] --p-query-delimiter TEXT The string used to delimit multiple search terms provided to include or exclude. This parameter should only need to be modified if the default delimiter (a comma) is used in the provided taxonomic annotations. [default: ','] --p-mode TEXT Choices('exact', 'contains') Mode for determining if a search term matches a taxonomic annotation. "contains" requires that the annotation has the term as a substring; "exact" requires that the annotation is a perfect match to a search term. [default: 'contains'] Outputs: --o-filtered-table ARTIFACT FeatureTable[Frequency] The taxonomy-filtered feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There were some problems with the command: (1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath Usage: qiime taxa barplot [OPTIONS] This visualizer produces an interactive barplot visualization of taxonomies. Interactive features include multi-level sorting, plot recoloring, sample relabeling, and SVG figure export. Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to visualize at various taxonomic levels. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --m-metadata-file METADATA... (multiple The sample metadata. arguments will be merged) [required] Outputs: --o-visualization VISUALIZATION [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There were some problems with the command: (1/2) Invalid value for '--i-table': 'table-no-Unassigned.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath Usage: qiime taxa collapse [OPTIONS] Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed. Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There were some problems with the command: (1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level1.qza as metadata: Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level1.qza There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/ Usage: qiime tools export [OPTIONS] Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level1.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help. Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level1.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS] Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample. Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level1.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level1.qza as metadata: Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level1.qza There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/ Usage: qiime tools export [OPTIONS] Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level1.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help. Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level1.biom' does not exist. cat: feature-table_absfreq_level1.tsv: No such file or directory cat: feature-table_absfreq_level1.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS] Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed. Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There were some problems with the command: (1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level2.qza as metadata: Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level2.qza There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/ Usage: qiime tools export [OPTIONS] Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level2.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help. Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level2.biom' does not exist. Saved Visualization to: demux_summary.qzv Usage: qiime feature-table relative-frequency [OPTIONS] Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample. Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level2.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level2.qza as metadata: Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level2.qza There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/ Usage: qiime feature-table summarize [OPTIONS] Generate visual and tabular summaries of a feature table. Inputs: --i-table ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence] The feature table to be summarized. [required] Parameters: --m-sample-metadata-file METADATA... (multiple The sample metadata. arguments will be merged) [optional] Outputs: --o-visualization VISUALIZATION [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--i-table': 'table.qza' is not a valid filepath Usage: qiime tools export [OPTIONS] Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level2.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: qiime feature-table tabulate-seqs [OPTIONS] Generate tabular view of feature identifier to sequence mapping, including links to BLAST each sequence against the NCBI nt database. Inputs: --i-data ARTIFACT FeatureData[Sequence | AlignedSequence] The feature sequences to be tabulated. [required] Outputs: --o-visualization VISUALIZATION [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--i-data': 'rep-seqs.qza' is not a valid filepath Usage: biom convert [OPTIONS] Try 'biom convert -h' for help. Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level2.biom' does not exist. Classifier 5 is not supported (choose between Blast and Vsearch); running default classifier Blast cat: feature-table_absfreq_level2.tsv: No such file or directory cat: feature-table_absfreq_level2.tsv: No such file or directory Usage: qiime taxa collapse [OPTIONS] Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed. Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There were some problems with the command: (1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_absfreq_level3.qza as metadata: Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level3.qza There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/ Usage: qiime tools export [OPTIONS] Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level3.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help. Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level3.biom' does not exist. Usage: qiime feature-table relative-frequency [OPTIONS] Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample. Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level3.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level3.qza as metadata: Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level3.qza There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/ Usage: qiime tools export [OPTIONS] Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level3.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: biom convert [OPTIONS] Try 'biom convert -h' for help. Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level3.biom' does not exist. cat: feature-table_absfreq_level3.tsv: No such file or directory cat: feature-table_absfreq_level3.tsv: No such file or directory Usage: qiime feature-classifier classify-consensus-blast [OPTIONS] Assign taxonomy to query sequences using BLAST+. Performs BLAST+ local alignment between query and reference_reads, then assigns consensus taxonomy to each query sequence from among maxaccepts hits, min_consensus of which share that taxonomic assignment. Note that maxaccepts selects the first N hits with > perc_identity similarity to query, not the top N matches. For top N hits, use classify-consensus-vsearch. Inputs: --i-query ARTIFACT FeatureData[Sequence] Sequences to classify taxonomically. [required] --i-reference-reads ARTIFACT FeatureData[Sequence] reference sequences. [required] --i-reference-taxonomy ARTIFACT FeatureData[Taxonomy] reference taxonomy labels. [required] Parameters: --p-maxaccepts INTEGER Maximum number of hits to keep for each query. Must Range(1, None) be in range [1, infinity]. BLAST will choose the first N hits in the reference database that exceed perc-identity similarity to query. [default: 10] --p-perc-identity PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if percent identity to query is lower. Must be in range [0.0, 1.0]. [default: 0.8] --p-query-cov PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if query alignment coverage per high-scoring pair is lower. Note: this uses blastn's qcov_hsp_perc parameter, and may not behave identically to the query-cov parameter used by classify-consensus-vsearch. Must be in range [0.0, 1.0]. [default: 0.8] --p-strand TEXT Choices('both', 'plus', 'minus') Align against reference sequences in forward ("plus"), reverse ("minus"), or both directions ("both"). [default: 'both'] --p-evalue NUMBER BLAST expectation value (E) threshold for saving hits. [default: 0.001] --p-min-consensus NUMBER Range(0.5, 1.0, inclusive_start=False, inclusive_end=True) Minimum fraction of assignments must match top hit to be accepted as consensus assignment. Must be in range (0.5, 1.0]. [default: 0.51] --p-unassignable-label TEXT [default: 'Unassigned'] Outputs: --o-classification ARTIFACT FeatureData[Taxonomy] Taxonomy classifications of query sequences. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There were some problems with the command: (1/3) Invalid value for '--i-query': 'rep-seqs.qza' is not a valid filepath (2/3) Invalid value for '--i-reference-taxonomy': '/home/qiime2' is not a QIIME 2 Artifact (.qza) (3/3) Invalid value for '--p-maxaccepts': received as an argument, which is incompatible with parameter type: Int % Range(1, None) Usage: qiime taxa collapse [OPTIONS] Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed. Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There were some problems with the command: (1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file taxonomy.qza as metadata: Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): taxonomy.qza There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/ There was an issue with loading the file table_collapsed_absfreq_level4.qza as metadata: Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level4.qza There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/ Usage: qiime tools export [OPTIONS] Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--input-path': File 'table_collapsed_absfreq_level4.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: qiime taxa barplot [OPTIONS] This visualizer produces an interactive barplot visualization of taxonomies. Interactive features include multi-level sorting, plot recoloring, sample relabeling, and SVG figure export. Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to visualize at various taxonomic levels. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --m-metadata-file METADATA... (multiple The sample metadata. arguments will be merged) [required] Outputs: --o-visualization VISUALIZATION [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There were some problems with the command: (1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath Usage: biom convert [OPTIONS] Try 'biom convert -h' for help. Error: Invalid value for '-i' / '--input-fp': File 'feature-table_absfreq_level4.biom' does not exist. Usage: qiime taxa filter-table [OPTIONS] This method filters features from a table based on their taxonomic annotations. Features can be retained in the resulting table by specifying one or more include search terms, and can be filtered out of the resulting table by specifying one or more exclude search terms. If both include and exclude are provided, the inclusion critera will be applied before the exclusion critera. Either include or exclude terms (or both) must be provided. Any samples that have a total frequency of zero after filtering will be removed from the resulting table. Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be filtered. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations for features that are not present in the feature table will be ignored. [required] Parameters: --p-include TEXT One or more search terms that indicate which taxa should be included in the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, all taxa will be included. [optional] --p-exclude TEXT One or more search terms that indicate which taxa should be excluded from the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, no taxa will be excluded. [optional] --p-query-delimiter TEXT The string used to delimit multiple search terms provided to include or exclude. This parameter should only need to be modified if the default delimiter (a comma) is used in the provided taxonomic annotations. [default: ','] --p-mode TEXT Choices('exact', 'contains') Mode for determining if a search term matches a taxonomic annotation. "contains" requires that the annotation has the term as a substring; "exact" requires that the annotation is a perfect match to a search term. [default: 'contains'] Outputs: --o-filtered-table ARTIFACT FeatureTable[Frequency] The taxonomy-filtered feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There were some problems with the command: (1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath Usage: qiime feature-table relative-frequency [OPTIONS] Convert frequencies to relative frequencies by dividing each frequency in a sample by the sum of frequencies in that sample. Inputs: --i-table ARTIFACT FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required] Outputs: --o-relative-frequency-table ARTIFACT FeatureTable[RelativeFrequency] The resulting relative frequency feature table. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--i-table': 'table_collapsed_absfreq_level4.qza' is not a valid filepath Usage: qiime taxa barplot [OPTIONS] This visualizer produces an interactive barplot visualization of taxonomies. Interactive features include multi-level sorting, plot recoloring, sample relabeling, and SVG figure export. Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to visualize at various taxonomic levels. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --m-metadata-file METADATA... (multiple The sample metadata. arguments will be merged) [required] Outputs: --o-visualization VISUALIZATION [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There were some problems with the command: (1/2) Invalid value for '--i-table': 'table-no-Unassigned.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath There was an issue with loading the file table_collapsed_relfreq_level4.qza as metadata: Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_relfreq_level4.qza There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/ Usage: qiime tools export [OPTIONS] Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be exported to [required] --output-format TEXT Format which the data should be exported as. This option cannot be used with Visualizations --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for '--input-path': File 'table_collapsed_relfreq_level4.qza' does not exist. mv: cannot stat 'feature-table.biom': No such file or directory Usage: qiime taxa collapse [OPTIONS] Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed. Inputs: --i-table ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required] --i-taxonomy ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required] Parameters: --p-level INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required] Outputs: --o-collapsed-table ARTIFACT FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. [required] Miscellaneous: --output-dir PATH Output unspecified results to a directory --verbose / --quiet Display verbose output to stdout and/or stderr during execution of this action. Or silence output if execution is successful (silence is golden). --examples Show usage examples and exit. --citations Show citations and exit. --help Show this message and exit. There were some problems with the command: (1/2) Invalid value for '--i-table': 'table.qza' is not a valid filepath (2/2) Invalid value for '--i-taxonomy': 'taxonomy.qza' is not a valid filepath Usage: biom convert [OPTIONS] Try 'biom convert -h' for help. Error: Invalid value for '-i' / '--input-fp': File 'feature-table_relfreq_level4.biom' does not exist. cat: feature-table_absfreq_level4.tsv: No such file or directory cat: feature-table_absfreq_level4.tsv: No such file or directory There was an issue with loading the file table_collapsed_absfreq_level1.qza as metadata: Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): table_collapsed_absfreq_level1.qza There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/ Usage: qiime tools export [OPTIONS] Exporting extracts (and optionally transforms) data stored inside an Artifact or Visualization. Note that Visualizations cannot be transformed with --output-format Options: --input-path ARTIFACT/VISUALIZATION Path to file that should be exported [required] --output-path PATH Path to file or directory where data should be

[MaestSi]

Your error is very similar to this one. I think the problem now is that you are not specifying the parameters correctly, with their full path (sample-metadata.tsv file included). Try to remove all files in the subsampling directory expect the fastq.gz files and run it again. But please, post also the command you used.

[dinavb]

The command I used was: nohup /home/qiime2/MetONTIIME/MetONTIIME.sh /home/qiime2/subsampling/ /home/qiime2/subsampling_analysis/sample-metadata.tsv /home/qiime2/silva_132_99_16S_sequence.qza /home/qiime2 silva_132_99_16S_taxonomy.qza 5 Vsearch 3 0.8 0.85

so it included all the full path, didn't it?

On Mon, Dec 14, 2020 at 10:10 AM Simone Maestri notifications@github.com wrote:

Your error is very similar to this one https://github.com/MaestSi/MetONTIIME/issues/22. I think the problem now is that you are not specifying the parameters correctly, with their full path (sample-metadata.tsv file included). Try to remove all files in the subsampling directory expect the fastq.gz files and run it again. But please, post also the command you used.

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[MaestSi]

Yes, it did. But a slash is missing between /home/qiime2 and silva_132_99_16S_taxonomy.qza, could it be the issue?

[dinavb]

Ok, so now I used the command: nohup /home/qiime2/MetONTIIME/MetONTIIME.sh /home/qiime2/subsampling/ /home/qiime2/subsampling_analysis/sample-metadata.tsv /home/qiime2/silva_132_99_16S_sequence.qza /home/qiime2/silva_132_99_16S_taxonomy.qza 5 Vsearch 3 0.8 0.85 nohup: ignoring input and appending output to 'nohup.out'

I attach the output. Where can I see the alpha and beta diversity? and how much RAM and what hardware requirements are required for analysis of the full data?

On Mon, Dec 14, 2020 at 12:09 PM Simone Maestri notifications@github.com wrote:

Yes, it did. But a slash is missing between /home/qiime2 and silva_132_99_16S_taxonomy.qza, could it be the issue?

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realpath: missing operand Try 'realpath --help' for more information. There was a problem importing /home/qiime2/subsampling//manifest.txt:

/home/qiime2/subsampling/manifest.txt is not a(n) SingleEndFastqManifestPhred33V2 file:

There was an issue with loading the metadata file:

Metadata must contain at least one ID.

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

Saved FeatureTable[Frequency] to: table_tmp.qza Saved FeatureData[Sequence] to: rep-seqs_tmp.qza Saved FeatureTable[Frequency] to: table.qza Saved FeatureData[Sequence] to: rep-seqs.qza Saved Visualization to: demux_summary.qzv Saved Visualization to: table.qzv Saved Visualization to: rep-seqs.qzv Saved FeatureData[Taxonomy] to: taxonomy.qza Saved Visualization to: taxonomy.qzv Saved Visualization to: taxa-bar-plots.qzv Saved FeatureTable[Frequency] to: table-no-Unassigned.qza Saved Visualization to: taxa-bar-plots-no-Unassigned.qzv Saved FeatureTable[Frequency] to: table_collapsed_absfreq_level1.qza Saved Visualization to: table_collapsed_absfreq_level1.qzv Exported table_collapsed_absfreq_level1.qza as BIOMV210DirFmt to directory . Saved FeatureTable[RelativeFrequency] to: table_collapsed_relfreq_level1.qza Saved Visualization to: table_collapsed_relfreq_level1.qzv Exported table_collapsed_relfreq_level1.qza as BIOMV210DirFmt to directory . Saved FeatureTable[Frequency] to: table_collapsed_absfreq_level2.qza Saved Visualization to: table_collapsed_absfreq_level2.qzv Exported table_collapsed_absfreq_level2.qza as BIOMV210DirFmt to directory . Saved FeatureTable[RelativeFrequency] to: table_collapsed_relfreq_level2.qza Saved Visualization to: table_collapsed_relfreq_level2.qzv Exported table_collapsed_relfreq_level2.qza as BIOMV210DirFmt to directory . Saved FeatureTable[Frequency] to: table_collapsed_absfreq_level3.qza Saved Visualization to: table_collapsed_absfreq_level3.qzv Exported table_collapsed_absfreq_level3.qza as BIOMV210DirFmt to directory . Saved FeatureTable[RelativeFrequency] to: table_collapsed_relfreq_level3.qza Saved Visualization to: table_collapsed_relfreq_level3.qzv Exported table_collapsed_relfreq_level3.qza as BIOMV210DirFmt to directory . Saved FeatureTable[Frequency] to: table_collapsed_absfreq_level4.qza Saved Visualization to: table_collapsed_absfreq_level4.qzv Exported table_collapsed_absfreq_level4.qza as BIOMV210DirFmt to directory . Saved FeatureTable[RelativeFrequency] to: table_collapsed_relfreq_level4.qza Saved Visualization to: table_collapsed_relfreq_level4.qzv Exported table_collapsed_relfreq_level4.qza as BIOMV210DirFmt to directory . Saved FeatureTable[Frequency] to: table_collapsed_absfreq_level5.qza Saved Visualization to: table_collapsed_absfreq_level5.qzv Exported table_collapsed_absfreq_level5.qza as BIOMV210DirFmt to directory . Saved FeatureTable[RelativeFrequency] to: table_collapsed_relfreq_level5.qza Saved Visualization to: table_collapsed_relfreq_level5.qzv Exported table_collapsed_relfreq_level5.qza as BIOMV210DirFmt to directory . Saved FeatureTable[Frequency] to: table_collapsed_absfreq_level6.qza Saved Visualization to: table_collapsed_absfreq_level6.qzv Exported table_collapsed_absfreq_level6.qza as BIOMV210DirFmt to directory . Saved FeatureTable[RelativeFrequency] to: table_collapsed_relfreq_level6.qza Saved Visualization to: table_collapsed_relfreq_level6.qzv Exported table_collapsed_relfreq_level6.qza as BIOMV210DirFmt to directory . Saved FeatureTable[Frequency] to: table_collapsed_absfreq_level7.qza Saved Visualization to: table_collapsed_absfreq_level7.qzv Exported table_collapsed_absfreq_level7.qza as BIOMV210DirFmt to directory . Saved FeatureTable[RelativeFrequency] to: table_collapsed_relfreq_level7.qza Saved Visualization to: table_collapsed_relfreq_level7.qzv Exported table_collapsed_relfreq_level7.qza as BIOMV210DirFmt to directory .

[MaestSi]

Do both directories /home/qiime2/subsampling and /home/qiime2/subsampling_analysis exist? I think I already answered the alpha and beta-diversity question in https://github.com/MaestSi/MetONTIIME/issues/20#issuecomment-733078566. Did you read it?

[dinavb]

Yes. both directories exist. How can I see the results? which files I should take to the qiime2 viewer? I tried some files but it only shows the code and not a graph. Thank you

On Mon, Dec 14, 2020 at 3:03 PM Simone Maestri notifications@github.com wrote:

Do both directories /home/qiime2/subsampling and /home/qiime2/subsampling_analysis exist? I think I already answered the alpha and beta-diversity question in #20 (comment) https://github.com/MaestSi/MetONTIIME/issues/20#issuecomment-733078566. Did you read it?

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[MaestSi]

If the pipeline ended successfully, you could upload to qiime2 viewer all .qzv files. In particular, you could upload file taxa-bar-plots.qzv and see the taxonomic composition of your samples.

[dinavb]

Dear Simone, It looks like it worked, I uploaded the taxa-bar-plots.qzv and it woerked. Now I tried the evaluate diversity with the following command: (MetONTIIME_env) qiime2@qiime2core2020-8:~$ Evaluate_diversity.sh -w /home/qiime2/subsampling -m /home/qiime2/subsampling_analysis/sample-metadata.tsv -d 100 -t 10 -c 1 Evaluate_diversity.sh: command not found

But received a message that the command wan not found

On Tue, Dec 15, 2020 at 11:32 AM Simone Maestri notifications@github.com wrote:

If the pipeline ended successfully, you could upload to qiime2 viewer all .qzv files. In particular, you could upload file taxa-bar-plots.qzv and see the taxonomic composition of your samples.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/MaestSi/MetONTIIME/issues/20#issuecomment-745167527, or unsubscribe https://github.com/notifications/unsubscribe-auth/AR34USSCILRCVFXBTYEI62DSU4UK3ANCNFSM4UAYZG7Q .

[MaestSi]

Hi, I think your MetONTIIME directory might not be in the PATH environment variable, therefore you need to specify the full path to the Evaluate_diversity.sh script or, if you are in the MetONTIIME directory, just use ./Evaluate_diversity.sh etc...

[dinavb]

(MetONTIIME_env) qiime2@qiime2core2020-8:~/MetONTIIME$ ./Evaluate_diversity.sh -w /home/qiime2/subsampling -m /home/qiime2/subsampling_analysis/sample-metadata.tsv -d 100 -t 10 -c 1 Working directory: /home/qiime2/subsampling Sample metadata: /home/qiime2/subsampling_analysis/sample-metadata.tsv Sampling depth: 100 reads Number of threads: 10 Clustering threshold: 1 realpath: missing operand Try 'realpath --help' for more information. There was a problem importing /home/qiime2/subsampling/manifest_100_subsampled.txt:

/home/qiime2/subsampling/manifest_100_subsampled.txt is not a(n) SingleEndFastqManifestPhred33V2 file:

There was an issue with loading the metadata file:

Metadata must contain at least one ID.

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2020.8/tutorials/metadata/

On Thu, Dec 17, 2020 at 9:47 AM Simone Maestri notifications@github.com wrote:

Hi, I think your MetONTIIME directory might not be in the PATH environment variable, therefore you need to specify the full path to the Evaluate_diversity.sh script or, if you are in the MetONTIIME directory, just use ./Evaluate_diversity.sh etc...

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[dinavb]

Dear Simone, I received the following error when I tried to run "evaluate diversity", what could be the problem now? Thank you!

(MetONTIIME_env) qiime2@qiime2core2020-8:~/MetONTIIME$ ./Evaluate_diversity.sh -w /home/qiime2/subsampling -m /home/qiime2/subsampling_analysis/sample-metadata.tsv -d 100 -t 10 -c 1 Working directory: /home/qiime2/subsampling Sample metadata: /home/qiime2/subsampling_analysis/sample-metadata.tsv Sampling depth: 100 reads Number of threads: 10 Clustering threshold: 1 realpath: missing operand Try 'realpath --help' for more information. There was a problem importing /home/qiime2/subsampling/manifest_100_subsampled.txt:

/home/qiime2/subsampling/manifest_100_subsampled.txt is not a(n) SingleEndFastqManifestPhred33V2 file:

There was an issue with loading the metadata file:

Metadata must contain at least one ID.

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

On Thu, Dec 17, 2020 at 9:47 AM Simone Maestri notifications@github.com wrote:

Hi, I think your MetONTIIME directory might not be in the PATH environment variable, therefore you need to specify the full path to the Evaluate_diversity.sh script or, if you are in the MetONTIIME directory, just use ./Evaluate_diversity.sh etc...

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[MaestSi]

Hi, I can't reproduce your issue with my data. You may try to remove the manifest file with: rm /home/qiime2/subsampling/manifest_100_subsampled.txt and then run again the same command (maybe with lower identity threshold than 1) You may also check that /home/qiime2/subsampling/manifest_100_subsampled.txt contains for each sample the ID (e.g. BC01) and the full path to the subsampled file (e.g. /path/to/BC01_100_subsampled.fastq.gz). Simone

[dinavb]

The "manifest_100_subsampled.txt" is empty,, I attach it

On Wed, Dec 23, 2020 at 10:41 AM Simone Maestri notifications@github.com wrote:

Hi, I can't reproduce your issue with my data. You may try to remove the manifest file with: rm /home/qiime2/subsampling/manifest_100_subsampled.txt and then run again the same command (maybe with lower identity threshold than 1) You may also check that /home/qiime2/subsampling/manifest_100_subsampled.txt contains for each sample the ID (e.g. BC01) and the full path to the subsampled file (e.g. /path/to/BC01_100_subsampled.fastq.gz). Simone

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sample-id absolute-filepath

[MaestSi]

Ok, I got it. The problem is that you are working with the subsampled dataset. You should rename your fastq.gz files so that they don't contain "subsampled" in the filename. Then it should work. P.s. delete file manifest_100_subsampled.txt before rerunning. Simone

[dinavb]

Where? I don't see any fastq.gz files that contain "subsampled" in the file name..

On Wed, Dec 23, 2020 at 12:17 PM Simone Maestri notifications@github.com wrote:

Ok, I got it. The problem is that you are working with the subsampled dataset. You should rename your fastq.gz files so that they don't contain "subsampled" in the filename. Then it should work. Simone

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[MaestSi]

Please, type this and tell me the output:

FASTQ_FILES=$(realpath $(find /home/qiime2/subsampling -maxdepth 1 | grep "\.fastq\.gz" | grep -v "subsampled\.fastq\.gz"))
echo $FASTQ_FILES | tr ' ' '\n'

Simone

[dinavb]

MetONTIIME_env) qiime2@qiime2core2020-8:~/MetONTIIME$ FASTQ_FILES=$(realpath $(find /home/qiime2/subsampling -maxdepth 1 | grep ".fastq.gz" | grep -v "subsampled.fastq.gz")) realpath: missing operand Try 'realpath --help' for more information.

On Wed, Dec 23, 2020 at 12:54 PM Simone Maestri notifications@github.com wrote:

Please, type this and tell me the output:

FASTQ_FILES=$(realpath $(find /home/qiime2/subsampling -maxdepth 1 | grep ".fastq.gz" | grep -v "subsampled.fastq.gz")) echo $FASTQ_FILES | tr ' ' '\n'

Simone

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[MaestSi]

This means that you don't have any fastq.gz files in the /home/qiime2/subsampling directory. If you confirm this is the case, this is totally expected. Simone

[dinavb]

Yes, I don't have any fastq/gz files in the subsampling directory. The fastq files are in the "barcodes" directory, while in the subsampling there are the qza and qzv and feature tables..

On Wed, Dec 23, 2020 at 1:55 PM Simone Maestri notifications@github.com wrote:

This means that you don't have any fastq.gz files in the /home/qiime2/subsampling directory. If you confirm this is the case, this is totally expected. Simone

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