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nf-core / ampliseq

Amplicon sequencing analysis workflow using DADA2 and QIIME2
https://nf-co.re/ampliseq
MIT License
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Process `NFCORE_AMPLISEQ:AMPLISEQ:METADATA_ALL (Metadata.tsv)` terminated with an error exit status (126) #590

Closed Truongphi20 closed 1 year ago

Truongphi20 commented 1 year ago

Description of the bug

Hi, I ran the following command to test ampliseq based on the documentary and got an error. Could someone tell me how to solve it? Thank you so much.

Command used and terminal output

$ nextflow run nf-core/ampliseq -r 2.5.0 -profile test,singularity  -c custom.config --outdir ./result -resume

And get an error

ERROR ~ Error executing process > 'NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:FORMAT_TAXONOMY_QIIME'

Caused by:
  Process `NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:FORMAT_TAXONOMY_QIIME` terminated with an error exit status (255)

Command executed:

  taxref_reformat_qiime_greengenes85.sh

      #Giving out information
      echo -e "--qiime_ref_taxonomy: greengenes85
  " >ref_taxonomy.txt
      echo -e "Title: Greengenes 16S - Version 13_8 - clustered at 85% similarity - for testing purposes only
  " >>ref_taxonomy.txt
      echo -e "Citation: McDonald, D., Price, M., Goodrich, J. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6, 610–618 (2012). https://doi.org/10.1038/ismej.2011.139
  " >>ref_taxonomy.txt
      echo "All entries: [title:Greengenes 16S - Version 13_8 - clustered at 85% similarity - for testing purposes only, file:[https://data.qiime2.org/2022.11/tutorials/training-feature-classifiers/85_otus.fasta, https://data.qiime2.org/2022.11/tutorials/training-feature-classifiers/85_otu_taxonomy.txt], citation:McDonald, D., Price, M., Goodrich, J. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6, 610–618 (2012). https://doi.org/10.1038/ismej.2011.139, fmtscript:taxref_reformat_qiime_greengenes85.sh]" >>ref_taxonomy.txt

      cat <<-END_VERSIONS > versions.yml
      "NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:FORMAT_TAXONOMY_QIIME":
          bash: $(bash --version | sed -n 1p | sed 's/GNU bash, version //g')
      END_VERSIONS

Command exit status:
  255

Command output:
  (empty)

Command error:
  FATAL:   container creation failed: mount /proc/self/fd/3->/usr/local/var/singularity/mnt/session/rootfs error: while mounting image /proc/self/fd/3: failed to find loop device: could not attach image file to loop device: no loop devices available

Work dir:
  /home/newstaff1/Desktop/myjob/Intern_diary/test_nf-core_ampliseq/work/a8/38de063f2a89bfaf8761c5c18e6277

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

 -- Check '.nextflow.log' file for details



### Relevant files

This is full output:

N E X T F L O W  ~  version 23.04.1
Launching `https://github.com/nf-core/ampliseq` [desperate_lumiere] DSL2 - revision: 78b7514cee [2.5.0]

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/ampliseq v2.5.0-g78b7514
------------------------------------------------------
Core Nextflow options
  revision                  : 2.5.0
  runName                   : desperate_lumiere
  containerEngine           : singularity
  launchDir                 : /home/newstaff1/Desktop/myjob/Intern_diary/test_nf-core_ampliseq
  workDir                   : /home/newstaff1/Desktop/myjob/Intern_diary/test_nf-core_ampliseq/work
  projectDir                : /home/newstaff1/.nextflow/assets/nf-core/ampliseq
  userName                  : newstaff1
  profile                   : test,singularity
  configFiles               : /home/newstaff1/.nextflow/assets/nf-core/ampliseq/nextflow.config, /home/newstaff1/Desktop/myjob/Intern_diary/test_nf-core_ampliseq/custom.config

Main arguments
  input                     : https://raw.githubusercontent.com/nf-core/test-datasets/ampliseq/samplesheets/Samplesheet.tsv
  FW_primer                 : GTGYCAGCMGCCGCGGTAA
  RV_primer                 : GGACTACNVGGGTWTCTAAT
  metadata                  : https://raw.githubusercontent.com/nf-core/test-datasets/ampliseq/samplesheets/Metadata.tsv
  outdir                    : ./result

Taxonomic database
  dada_ref_taxonomy         : gtdb
  cut_dada_ref_taxonomy     : true
  qiime_ref_taxonomy        : greengenes85

ASV filtering
  filter_ssu                : bac
  max_len_asv               : 255
  min_frequency             : 10
  min_samples               : 2

Downstream analysis
  metadata_category_barplot : treatment1,badpairwise10
  qiime_adonis_formula      : treatment1,mix8
  sbdiexport                : true
  dada_tax_agglom_max       : 4
  qiime_tax_agglom_max      : 4

Max job request options
  max_cpus                  : 2
  max_memory                : 6.GB
  max_time                  : 6.h

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/ampliseq for your analysis please cite:

* The pipeline publication
  https://doi.org/10.3389/fmicb.2020.550420

* The pipeline
  https://doi.org/10.5281/zenodo.1493841

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/nf-core/ampliseq/blob/master/CITATIONS.md
------------------------------------------------------
WARN: No DADA2 cutoffs were specified (`--trunclenf` & `--trunclenr`), therefore reads will be truncated where median quality drops below 25 (defined by `--trunc_qmin`) but at least a fraction of 0.75 (defined by `--trunc_rmin`) of the reads will be retained.
The chosen cutoffs do not account for required overlap for merging, therefore DADA2 might have poor merging efficiency or even fail.

[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES                    -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FASTQC                                   -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC         -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_STD   -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_MERGE -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY1       -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:TRUNCLEN             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES                       -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FASTQC                                      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC            -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_STD      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_MERGE    -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY1          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:TRUNCLEN                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_FILTNTRIM         -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY2          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ERR                                   -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_DENOISING                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_RMCHIMERA                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_STATS                                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_MERGE                                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_STD                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAP                                     -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAPSUMMARY                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_SSU                                  -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERSSU                       -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_LEN_ASV                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERLENASV                    -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FORMAT_TAXONOMY                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_TAXONOMY                           -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES                       -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FASTQC                                      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC            -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_STD      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_MERGE    -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY1          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:TRUNCLEN                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_FILTNTRIM         -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY2          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ERR                                   -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_DENOISING                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_RMCHIMERA                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_STATS                                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_MERGE                                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_STD                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAP                                     -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAPSUMMARY                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_SSU                                  -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERSSU                       -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_LEN_ASV                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERLENASV                    -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FORMAT_TAXONOMY                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_TAXONOMY                           -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ADDSPECIES                            -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:FORMAT_TAXONOMY_QIIME        -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_EXTRACT               -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES                       -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FASTQC                                      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC            -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_STD      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_MERGE    -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY1          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:TRUNCLEN                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_FILTNTRIM         -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY2          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ERR                                   -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_DENOISING                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_RMCHIMERA                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_STATS                                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_MERGE                                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_STD                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAP                                     -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAPSUMMARY                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_SSU                                  -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERSSU                       -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_LEN_ASV                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERLENASV                    -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FORMAT_TAXONOMY                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_TAXONOMY                           -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ADDSPECIES                            -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:FORMAT_TAXONOMY_QIIME        -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_EXTRACT               -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_TRAIN                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TAXONOMY:QIIME2_INSEQ                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TAXONOMY:QIIME2_CLASSIFY             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INASV                                -
executor >  local (1)
[de/fea5ad] process > NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES (sampleID_1)          [  0%] 0 of 1
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FASTQC                                      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC            -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_STD      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_MERGE    -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY1          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:TRUNCLEN                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_FILTNTRIM         -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY2          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ERR                                   -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_DENOISING                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_RMCHIMERA                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_STATS                                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_MERGE                                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_STD                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAP                                     -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAPSUMMARY                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_SSU                                  -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERSSU                       -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_LEN_ASV                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERLENASV                    -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FORMAT_TAXONOMY                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_TAXONOMY                           -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ADDSPECIES                            -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:FORMAT_TAXONOMY_QIIME        -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_EXTRACT               -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_TRAIN                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TAXONOMY:QIIME2_INSEQ                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TAXONOMY:QIIME2_CLASSIFY             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INASV                                -
executor >  local (1)
[de/fea5ad] process > NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES (sampleID_1)          [100%] 1 of 1
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FASTQC                                      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC            -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_STD      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_MERGE    -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY1          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:TRUNCLEN                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_FILTNTRIM         -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY2          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ERR                                   -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_DENOISING                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_RMCHIMERA                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_STATS                                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_MERGE                                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_STD                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAP                                     -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAPSUMMARY                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_SSU                                  -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERSSU                       -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_LEN_ASV                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERLENASV                    -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FORMAT_TAXONOMY                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_TAXONOMY                           -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ADDSPECIES                            -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:FORMAT_TAXONOMY_QIIME        -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_EXTRACT               -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_TRAIN                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TAXONOMY:QIIME2_INSEQ                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TAXONOMY:QIIME2_CLASSIFY             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INASV                                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INSEQ                                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INTAX                                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_FILTERTAXA                           -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_STATS                                -
executor >  local (2)
[a2/2721f4] process > NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES (sampleID_1a)         [ 50%] 1 of 2
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FASTQC                                      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC            -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_STD      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_MERGE    -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY1          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:TRUNCLEN                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_FILTNTRIM         -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY2          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ERR                                   -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_DENOISING                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_RMCHIMERA                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_STATS                                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_MERGE                                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_STD                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAP                                     -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAPSUMMARY                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_SSU                                  -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERSSU                       -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_LEN_ASV                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERLENASV                    -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FORMAT_TAXONOMY                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_TAXONOMY                           -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ADDSPECIES                            -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:FORMAT_TAXONOMY_QIIME        -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_EXTRACT               -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_TRAIN                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TAXONOMY:QIIME2_INSEQ                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TAXONOMY:QIIME2_CLASSIFY             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INASV                                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INSEQ                                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INTAX                                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_FILTERTAXA                           -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_STATS                                -
executor >  local (2)
[a2/2721f4] process > NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES (sampleID_1a)         [100%] 2 of 2
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FASTQC                                      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC            -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_STD      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_MERGE    -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY1          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:TRUNCLEN                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_FILTNTRIM         -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY2          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ERR                                   -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_DENOISING                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_RMCHIMERA                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_STATS                                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_MERGE                                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_STD                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAP                                     -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAPSUMMARY                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_SSU                                  -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERSSU                       -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_LEN_ASV                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERLENASV                    -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FORMAT_TAXONOMY                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_TAXONOMY                           -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ADDSPECIES                            -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:FORMAT_TAXONOMY_QIIME        -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_EXTRACT               -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_TRAIN                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TAXONOMY:QIIME2_INSEQ                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TAXONOMY:QIIME2_CLASSIFY             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INASV                                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INSEQ                                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INTAX                                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_FILTERTAXA                           -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_STATS                                -
executor >  local (4)
[e8/949594] process > NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES (sampleID_2a)         [ 66%] 2 of 3
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FASTQC                                      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC            -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_STD      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_MERGE    -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY1          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:TRUNCLEN                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_FILTNTRIM         -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY2          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ERR                                   -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_DENOISING                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_RMCHIMERA                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_STATS                                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_MERGE                                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_STD                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAP                                     -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAPSUMMARY                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_SSU                                  -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERSSU                       -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_LEN_ASV                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERLENASV                    -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FORMAT_TAXONOMY                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_TAXONOMY                           -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ADDSPECIES                            -
[a8/38de06] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:FORMAT_TAXONOMY_QIIME        [  0%] 0 of 1
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_EXTRACT               -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_TRAIN                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TAXONOMY:QIIME2_INSEQ                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TAXONOMY:QIIME2_CLASSIFY             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INASV                                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INSEQ                                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INTAX                                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_FILTERTAXA                           -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_STATS                                -
executor >  local (4)
[e8/949594] process > NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES (sampleID_2a)         [ 66%] 2 of 3
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FASTQC                                      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC            -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_STD      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_MERGE    -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY1          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:TRUNCLEN                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_FILTNTRIM         -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY2          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ERR                                   -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_DENOISING                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_RMCHIMERA                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_STATS                                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_MERGE                                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_STD                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAP                                     -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAPSUMMARY                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_SSU                                  -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERSSU                       -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_LEN_ASV                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERLENASV                    -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FORMAT_TAXONOMY                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_TAXONOMY                           -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ADDSPECIES                            -
[a8/38de06] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:FORMAT_TAXONOMY_QIIME        [  0%] 0 of 1
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_EXTRACT               -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_TRAIN                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TAXONOMY:QIIME2_INSEQ                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TAXONOMY:QIIME2_CLASSIFY             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INASV                                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INSEQ                                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INTAX                                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_FILTERTAXA                           -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_STATS                                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERTAXA                      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_ABSOLUTE        -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_RELASV          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_RELTAX          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_QIIME2          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_DADA2           -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOT                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOTAVG:QIIME2_INASV_BPAVG        -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOTAVG:QIIME2_FEATURETABLE_GROUP -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOTAVG:QIIME2_BPAVG              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:METADATA_ALL                                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:METADATA_PAIRWISE                           -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_TREE                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_ALPHARAREFACTION    -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_DIVERSITY_CORE      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_DIVERSITY_ALPHA     -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_DIVERSITY_BETA      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_DIVERSITY_ADONIS    -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_DIVERSITY_BETAORD   -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_FILTERSAMPLES_ANCOM     -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_ANCOM_TAX               -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_ANCOM_ASV               -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:SBDIEXPORT                                  -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:SBDIEXPORTREANNOTATE                        -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUSTOM_DUMPSOFTWAREVERSIONS                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MULTIQC                                     -
Use DADA2 taxonomy classification
Pulling Singularity image https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0 [cache /home/newstaff1/Desktop/myjob/Intern_diary/test_nf-core_ampliseq/work/singularity/depot.galaxyproject.org-singularity-bioconductor-dada2-1.22.0--r41h399db7b_0.img]
Pulling Singularity image https://depot.galaxyproject.org/singularity/cutadapt:3.4--py39h38f01e4_1 [cache /home/newstaff1/Desktop/myjob/Intern_diary/test_nf-core_ampliseq/work/singularity/depot.galaxyproject.org-singularity-cutadapt-3.4--py39h38f01e4_1.img]
Pulling Singularity image https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0 [cache /home/newstaff1/Desktop/myjob/Intern_diary/test_nf-core_ampliseq/work/singularity/depot.galaxyproject.org-singularity-fastqc-0.11.9--0.img]
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /home/newstaff1/Desktop/myjob/Intern_diary/test_nf-core_ampliseq/work/singularity -- Use the environment variable NXF_SINGULARITY_CACHEDIR to specify a different location
ERROR ~ Error executing process > 'NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:FORMAT_TAXONOMY_QIIME'

Caused by:
  Process `NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:FORMAT_TAXONOMY_QIIME` terminated with an error exit status (255)

Command executed:

  taxref_reformat_qiime_greengenes85.sh

executor >  local (4)
[e8/949594] process > NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES (sampleID_2a)         [100%] 3 of 3
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FASTQC                                      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC            -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_STD      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_MERGE    -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY1          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:TRUNCLEN                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_FILTNTRIM         -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY2          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ERR                                   -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_DENOISING                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_RMCHIMERA                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_STATS                                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_MERGE                                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_STD                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAP                                     -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAPSUMMARY                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_SSU                                  -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERSSU                       -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_LEN_ASV                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERLENASV                    -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FORMAT_TAXONOMY                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_TAXONOMY                           -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ADDSPECIES                            -
[a8/38de06] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:FORMAT_TAXONOMY_QIIME        [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_EXTRACT               -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_TRAIN                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TAXONOMY:QIIME2_INSEQ                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TAXONOMY:QIIME2_CLASSIFY             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INASV                                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INSEQ                                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INTAX                                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_FILTERTAXA                           -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_STATS                                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERTAXA                      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_ABSOLUTE        -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_RELASV          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_RELTAX          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_QIIME2          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_DADA2           -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOT                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOTAVG:QIIME2_INASV_BPAVG        -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOTAVG:QIIME2_FEATURETABLE_GROUP -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOTAVG:QIIME2_BPAVG              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:METADATA_ALL                                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:METADATA_PAIRWISE                           -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_TREE                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_ALPHARAREFACTION    -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_DIVERSITY_CORE      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_DIVERSITY_ALPHA     -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_DIVERSITY_BETA      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_DIVERSITY_ADONIS    -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_DIVERSITY_BETAORD   -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_FILTERSAMPLES_ANCOM     -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_ANCOM_TAX               -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_ANCOM_ASV               -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:SBDIEXPORT                                  -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:SBDIEXPORTREANNOTATE                        -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUSTOM_DUMPSOFTWAREVERSIONS                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MULTIQC                                     -
Use DADA2 taxonomy classification
Pulling Singularity image https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0 [cache /home/newstaff1/Desktop/myjob/Intern_diary/test_nf-core_ampliseq/work/singularity/depot.galaxyproject.org-singularity-bioconductor-dada2-1.22.0--r41h399db7b_0.img]
Pulling Singularity image https://depot.galaxyproject.org/singularity/cutadapt:3.4--py39h38f01e4_1 [cache /home/newstaff1/Desktop/myjob/Intern_diary/test_nf-core_ampliseq/work/singularity/depot.galaxyproject.org-singularity-cutadapt-3.4--py39h38f01e4_1.img]
Pulling Singularity image https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0 [cache /home/newstaff1/Desktop/myjob/Intern_diary/test_nf-core_ampliseq/work/singularity/depot.galaxyproject.org-singularity-fastqc-0.11.9--0.img]
Execution cancelled -- Finishing pending tasks before exit
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /home/newstaff1/Desktop/myjob/Intern_diary/test_nf-core_ampliseq/work/singularity -- Use the environment variable NXF_SINGULARITY_CACHEDIR to specify a different location
ERROR ~ Error executing process > 'NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:FORMAT_TAXONOMY_QIIME'

Caused by:
  Process `NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:FORMAT_TAXONOMY_QIIME` terminated with an error exit status (255)

Command executed:

  taxref_reformat_qiime_greengenes85.sh

executor >  local (4)
[e8/949594] process > NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES (sampleID_2a)         [ 75%] 3 of 4
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FASTQC                                      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC            -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_STD      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_MERGE    -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY1          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:TRUNCLEN                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_FILTNTRIM         -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY2          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ERR                                   -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_DENOISING                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_RMCHIMERA                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_STATS                                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_MERGE                                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_STD                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAP                                     -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAPSUMMARY                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_SSU                                  -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERSSU                       -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_LEN_ASV                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERLENASV                    -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FORMAT_TAXONOMY                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_TAXONOMY                           -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ADDSPECIES                            -
[a8/38de06] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:FORMAT_TAXONOMY_QIIME        [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_EXTRACT               -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_TRAIN                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TAXONOMY:QIIME2_INSEQ                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TAXONOMY:QIIME2_CLASSIFY             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INASV                                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INSEQ                                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INTAX                                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_FILTERTAXA                           -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_STATS                                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERTAXA                      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_ABSOLUTE        -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_RELASV          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_RELTAX          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_QIIME2          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_DADA2           -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOT                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOTAVG:QIIME2_INASV_BPAVG        -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOTAVG:QIIME2_FEATURETABLE_GROUP -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOTAVG:QIIME2_BPAVG              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:METADATA_ALL                                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:METADATA_PAIRWISE                           -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_TREE                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_ALPHARAREFACTION    -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_DIVERSITY_CORE      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_DIVERSITY_ALPHA     -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_DIVERSITY_BETA      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_DIVERSITY_ADONIS    -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_DIVERSITY_BETAORD   -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_FILTERSAMPLES_ANCOM     -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_ANCOM_TAX               -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_ANCOM_ASV               -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:SBDIEXPORT                                  -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:SBDIEXPORTREANNOTATE                        -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUSTOM_DUMPSOFTWAREVERSIONS                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MULTIQC                                     -
Use DADA2 taxonomy classification
Pulling Singularity image https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0 [cache /home/newstaff1/Desktop/myjob/Intern_diary/test_nf-core_ampliseq/work/singularity/depot.galaxyproject.org-singularity-bioconductor-dada2-1.22.0--r41h399db7b_0.img]
Pulling Singularity image https://depot.galaxyproject.org/singularity/cutadapt:3.4--py39h38f01e4_1 [cache /home/newstaff1/Desktop/myjob/Intern_diary/test_nf-core_ampliseq/work/singularity/depot.galaxyproject.org-singularity-cutadapt-3.4--py39h38f01e4_1.img]
Pulling Singularity image https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0 [cache /home/newstaff1/Desktop/myjob/Intern_diary/test_nf-core_ampliseq/work/singularity/depot.galaxyproject.org-singularity-fastqc-0.11.9--0.img]
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/ampliseq] Pipeline completed with errors-
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /home/newstaff1/Desktop/myjob/Intern_diary/test_nf-core_ampliseq/work/singularity -- Use the environment variable NXF_SINGULARITY_CACHEDIR to specify a different location
ERROR ~ Error executing process > 'NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:FORMAT_TAXONOMY_QIIME'

Caused by:
  Process `NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:FORMAT_TAXONOMY_QIIME` terminated with an error exit status (255)

Command executed:

  taxref_reformat_qiime_greengenes85.sh

executor >  local (4)
[e8/949594] process > NFCORE_AMPLISEQ:AMPLISEQ:RENAME_RAW_DATA_FILES (sampleID_2a)         [ 75%] 3 of 4
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FASTQC                                      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_BASIC            -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_STD      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_WORKFLOW:CUTADAPT_SUMMARY_MERGE    -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY1          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:TRUNCLEN                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_FILTNTRIM         -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_PREPROCESSING:DADA2_QUALITY2          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ERR                                   -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_DENOISING                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_RMCHIMERA                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_STATS                                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_MERGE                                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_STD                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAP                                     -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:BARRNAPSUMMARY                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_SSU                                  -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERSSU                       -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_LEN_ASV                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERLENASV                    -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FORMAT_TAXONOMY                             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUTADAPT_TAXONOMY                           -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_TAXONOMY                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:DADA2_ADDSPECIES                            -
[a8/38de06] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:FORMAT_TAXONOMY_QIIME        [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_EXTRACT               -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:QIIME2_TRAIN                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TAXONOMY:QIIME2_INSEQ                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_TAXONOMY:QIIME2_CLASSIFY             -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INASV                                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INSEQ                                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_INTAX                                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_FILTERTAXA                           -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:FILTER_STATS                                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MERGE_STATS_FILTERTAXA                      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_ABSOLUTE        -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_RELASV          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:QIIME2_EXPORT_RELTAX          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_QIIME2          -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_EXPORT:COMBINE_TABLE_DADA2           -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOT                              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOTAVG:QIIME2_INASV_BPAVG        -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOTAVG:QIIME2_FEATURETABLE_GROUP -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_BARPLOTAVG:QIIME2_BPAVG              -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:METADATA_ALL                                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:METADATA_PAIRWISE                           -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_TREE                -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_ALPHARAREFACTION    -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_DIVERSITY_CORE      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_DIVERSITY_ALPHA     -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_DIVERSITY_BETA      -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_DIVERSITY_ADONIS    -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_DIVERSITY:QIIME2_DIVERSITY_BETAORD   -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_FILTERSAMPLES_ANCOM     -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_ANCOM_TAX               -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_ANCOM_ASV               -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:SBDIEXPORT                                  -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:SBDIEXPORTREANNOTATE                        -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:CUSTOM_DUMPSOFTWAREVERSIONS                 -
[-        ] process > NFCORE_AMPLISEQ:AMPLISEQ:MULTIQC                                     -
Use DADA2 taxonomy classification
Pulling Singularity image https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0 [cache /home/newstaff1/Desktop/myjob/Intern_diary/test_nf-core_ampliseq/work/singularity/depot.galaxyproject.org-singularity-bioconductor-dada2-1.22.0--r41h399db7b_0.img]
Pulling Singularity image https://depot.galaxyproject.org/singularity/cutadapt:3.4--py39h38f01e4_1 [cache /home/newstaff1/Desktop/myjob/Intern_diary/test_nf-core_ampliseq/work/singularity/depot.galaxyproject.org-singularity-cutadapt-3.4--py39h38f01e4_1.img]
Pulling Singularity image https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0 [cache /home/newstaff1/Desktop/myjob/Intern_diary/test_nf-core_ampliseq/work/singularity/depot.galaxyproject.org-singularity-fastqc-0.11.9--0.img]
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/ampliseq] Pipeline completed with errors-
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /home/newstaff1/Desktop/myjob/Intern_diary/test_nf-core_ampliseq/work/singularity -- Use the environment variable NXF_SINGULARITY_CACHEDIR to specify a different location
ERROR ~ Error executing process > 'NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:FORMAT_TAXONOMY_QIIME'

Caused by:
  Process `NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:FORMAT_TAXONOMY_QIIME` terminated with an error exit status (255)

Command executed:

  taxref_reformat_qiime_greengenes85.sh

      #Giving out information
      echo -e "--qiime_ref_taxonomy: greengenes85
  " >ref_taxonomy.txt
      echo -e "Title: Greengenes 16S - Version 13_8 - clustered at 85% similarity - for testing purposes only
  " >>ref_taxonomy.txt
      echo -e "Citation: McDonald, D., Price, M., Goodrich, J. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6, 610–618 (2012). https://doi.org/10.1038/ismej.2011.139
  " >>ref_taxonomy.txt
      echo "All entries: [title:Greengenes 16S - Version 13_8 - clustered at 85% similarity - for testing purposes only, file:[https://data.qiime2.org/2022.11/tutorials/training-feature-classifiers/85_otus.fasta, https://data.qiime2.org/2022.11/tutorials/training-feature-classifiers/85_otu_taxonomy.txt], citation:McDonald, D., Price, M., Goodrich, J. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6, 610–618 (2012). https://doi.org/10.1038/ismej.2011.139, fmtscript:taxref_reformat_qiime_greengenes85.sh]" >>ref_taxonomy.txt

      cat <<-END_VERSIONS > versions.yml
      "NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_PREPTAX:FORMAT_TAXONOMY_QIIME":
          bash: $(bash --version | sed -n 1p | sed 's/GNU bash, version //g')
      END_VERSIONS

Command exit status:
  255

Command output:
  (empty)

Command error:
  FATAL:   container creation failed: mount /proc/self/fd/3->/usr/local/var/singularity/mnt/session/rootfs error: while mounting image /proc/self/fd/3: failed to find loop device: could not attach image file to loop device: no loop devices available

Work dir:
  /home/newstaff1/Desktop/myjob/Intern_diary/test_nf-core_ampliseq/work/a8/38de063f2a89bfaf8761c5c18e6277

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

 -- Check '.nextflow.log' file for details
Staging foreign file: https://data.ace.uq.edu.au/public/gtdb/data/releases/release207/207.0/genomic_files_reps/bac120_ssu_reps_r207.tar.gz
Waiting for file transfers to complete (1 files)

### System information

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/ampliseq v2.5.0-g78b7514
------------------------------------------------------
Core Nextflow options
  revision                  : 2.5.0
  runName                   : desperate_lumiere
  containerEngine           : singularity
  launchDir                 : /home/newstaff1/Desktop/myjob/Intern_diary/test_nf-core_ampliseq
  workDir                   : /home/newstaff1/Desktop/myjob/Intern_diary/test_nf-core_ampliseq/work
  projectDir                : /home/newstaff1/.nextflow/assets/nf-core/ampliseq
  userName                  : newstaff1
  profile                   : test,singularity
  configFiles               : /home/newstaff1/.nextflow/assets/nf-core/ampliseq/nextflow.config, /home/newstaff1/Desktop/myjob/Intern_diary/test_nf-core_ampliseq/custom.config

Main arguments
  input                     : https://raw.githubusercontent.com/nf-core/test-datasets/ampliseq/samplesheets/Samplesheet.tsv
  FW_primer                 : GTGYCAGCMGCCGCGGTAA
  RV_primer                 : GGACTACNVGGGTWTCTAAT
  metadata                  : https://raw.githubusercontent.com/nf-core/test-datasets/ampliseq/samplesheets/Metadata.tsv
  outdir                    : ./result

Taxonomic database
  dada_ref_taxonomy         : gtdb
  cut_dada_ref_taxonomy     : true
  qiime_ref_taxonomy        : greengenes85

ASV filtering
  filter_ssu                : bac
  max_len_asv               : 255
  min_frequency             : 10
  min_samples               : 2

Downstream analysis
  metadata_category_barplot : treatment1,badpairwise10
  qiime_adonis_formula      : treatment1,mix8
  sbdiexport                : true
  dada_tax_agglom_max       : 4
  qiime_tax_agglom_max      : 4

Max job request options
  max_cpus                  : 2
  max_memory                : 6.GB
  max_time                  : 6.h

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function
d4straub commented 1 year ago

Hi there, not sure whats wrong, did you already or could you use -resume (or just restart) to make sure thats not a temporal hiccup of internet connectivity or such?

FATAL: container creation failed: mount /proc/self/fd/3->/usr/local/var/singularity/mnt/session/rootfs error: while mounting image /proc/self/fd/3: failed to find loop device: could not attach image file to loop device: no loop devices available

sounds like a problem of the container or container engine.

Might be related to https://github.com/sylabs/singularity/issues/67 which hints to a malfunction of singularity.

d4straub commented 1 year ago

I close that now, please feel free to open another issue in case you encounter another challenge.