Merritt-Brian
commented
9 months ago @erinyoung Can you check if the FASTA file in downloads is empty or not? Also, can you place your execution report (pipeline_info/*html file) here?
Closed erinyoung closed 7 months ago
Merritt-Brian
commented
9 months ago @erinyoung Can you check if the FASTA file in downloads is empty or not? Also, can you place your execution report (pipeline_info/*html file) here?
erinyoung
commented
9 months ago The fasta in downloads isn't empty:
$ wc -l download/*
1767486 download/sample59.output.references.fasta
2526991 download/taxonomy.tab
4294477 totalI added a .txt extension to each of the files in pipeline_info and am sharing them here (github doesn't like .html files)
execution_timeline_2023-11-22_12-12-17.html.txt
execution_trace_2023-11-22_12-12-17.txt.txt
Merritt-Brian
commented
9 months ago This looks like a potential issue with feeding in outputs of a previous module (that may or may not have failed) to later channels. I.e.
[ ! -f sample58.fastq.gz ] && ln -sf sample58.fastq.gz sample58.fastq.gz
fastp \
--in1 sample58.fastq.gz \
--out1 sample58.fastp.fastq.gz \
--thread 6 \
--json sample58.fastp.json \
--html sample58.fastp.html \
\
\
-q 7 \
2> sample58.fastp.log
cat <<-END_VERSIONS > versions.yml
"NFCORE_TAXTRIAGE:TAXTRIAGE:FASTP":
fastp: $(fastp --version 2>&1 | sed -e "s/fastp //g")
Shows during Sample58's QC processing fails. One thing to look at is if Sample58 has the proper location in the samplesheet. Otherwise, check on the quality metrics for that sample and see if low Q leads to no "passed" output. You can also skip QC filtering of low quality reads with --skip_fastp
hkunerth
commented
9 months ago I'm still running in to this issue. It doesn't appear that my sequence quality is the issue, though I'd be happy to look if you can confirm where I should expect to see the "passed" output. From what I can tell all these files exist and are populated:
ERROR ~ Invalid method invocation call with arguments: [[id:2014317068_Lung_RNA, single_end:false, platform:ILLUMINA, fastq_1:/home/mdh/shared/taxtriage/taxtriage_231211_dev/samples/2014317068_Lung_RNA.Illumina.kraken.dehosted_1.fastq.gz, fastq_2:/home/mdh/shared/taxtriage/taxtriage_231211_dev/samples/2014317068_Lung_RNA.Illumina.kraken.dehosted_2.fastq.gz, trim:true, directory:false, sequencing_summary:null], /panfs/jay/groups/32/mdh/shared/taxtriage/taxtriage_231211_dev/work/38/d8ae97d6a54b7883016f5e55824cfb/2014317068_Lung_RNA.top_report.tsv, [/panfs/jay/groups/32/mdh/shared/taxtriage/taxtriage_231211_dev/work/fd/fd855ce65a96ed33d70499cbcbdf9c/2014317068_Lung_RNA.classified_1.fastq.gz, /panfs/jay/groups/32/mdh/shared/taxtriage/taxtriage_231211_dev/work/fd/fd855ce65a96ed33d70499cbcbdf9c/2014317068_Lung_RNA.classified_2.fastq.gz], /panfs/jay/groups/32/mdh/shared/taxtriage/taxtriage_231211_dev/work/ed/c3980dcd017cd19e40ed8ae2b72c3c/2014317068_Lung_RNA.output.references.fasta] (java.util.ArrayList) on _closure22 type
` Is there anything else I could provide to help clarify the source of the issue?
erinyoung
commented
9 months ago Shows during Sample58's QC processing fails. One thing to look at is if Sample58 has the proper location in the samplesheet. Otherwise, check on the quality metrics for that sample and see if low Q leads to no "passed" output. You can also skip QC filtering of low quality reads with --skip_fastp
Did you look over my sample sheet somewhere? I've attached it above.
Merritt-Brian
commented
9 months ago @erinyoung Your samplesheet looks good, provided that you're running that command from the CLI WITH Tower and there are no networking issues with uploads.
Have you attempted the --skip_fastp yet? Currently fastp trims to minq of 7 Or potentially set "trim" to FALSE in the Samplesheet?
@hkunerth youre issue seem's to be unrelated to this problem, will address in #28
erinyoung
commented
9 months ago I think I found at least two issues : you don't have default values for some of the parameters
WARN: Access to undefined parameter `skip_assembly` -- Initialise it to a default value eg. `params.skip_assembly = some_value`
WARN: Access to undefined parameter `top_hits_count` -- Initialise it to a default value eg. `params.top_hits_count = some_value`Also, I tried running the workflow without -with-tower and ran into the same error.
erinyoung
commented
9 months ago I adjusted my command to add in some values for the warnings that I was seeing, and now I get different things printed to stdout!
nextflow run jhuapl-bio/taxtriage --input samplesheet.csv --outdir taxtriage -profile docker -resume --db /Volumes/IDGenomics_NAS/Data/kraken2_db/2023-06-05 -r main --skip_assembly false --top_hits_count 3N E X T F L O W ~ version 23.10.0
NOTE: Your local project version looks outdated - a different revision is available in the remote repository [a603a52746]
Launching `https://github.com/jhuapl-bio/taxtriage` [friendly_booth] DSL2 - revision: 0e260b40d0 [main]
WARN: Found unexpected parameters:
* --max_time: 240.h
* --max_cpus: 16
* --max_memory: 1380.GB
* --config_profile_name: null
* --config_profile_url: null
* --config_profile_contact: null
* --config_profile_description: null
* --custom_config_base: https://raw.githubusercontent.com/nf-core/configs/master
* --custom_config_version: master
* --enable_conda: false
* --show_hidden_params: false
* --validate_params: true
* --help: false
* --monochrome_logs: false
* --plaintext_email: false
* --email_on_fail: null
* --publish_dir_mode: copy
* --tracedir: taxtriage/pipeline_info
* --max_multiqc_email_size: 25.MB
* --multiqc_logo: null
* --skip_variants: null
* --skip_consensus: null
* --subsample: null
* --top_hits_counts: null
* --minq: null
* --three_prime_clip_r2: null
* --three_prime_clip_r1: null
* --clip_r1: null
* --clip_r2: null
* --spades_hmm: null
* --remove_reference_file: null
- Ignore this warning: params.schema_ignore_params = "max_time,max_cpus,max_memory,config_profile_name,config_profile_url,config_profile_contact,config_profile_description,custom_config_base,custom_config_version,enable_conda,show_hidden_params,validate_params,help,monochrome_logs,plaintext_email,email_on_fail,publish_dir_mode,tracedir,max_multiqc_email_size,multiqc_logo,skip_variants,skip_consensus,subsample,top_hits_counts,minq,three_prime_clip_r2,three_prime_clip_r1,clip_r1,clip_r2,spades_hmm,remove_reference_file"
------------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/taxtriage v1.0dev
------------------------------------------------------
Core Nextflow options
revision : main
runName : friendly_booth
containerEngine: docker
launchDir : /Volumes/BioNGS_1/UT-P2S01293-231116/UT-P2S01293-231116/20231116_2158_P2S-01293-B_PAS24124_ea91207e
workDir : /Volumes/BioNGS_1/UT-P2S01293-231116/UT-P2S01293-231116/20231116_2158_P2S-01293-B_PAS24124_ea91207e/work
projectDir : /home/eriny/.nextflow/assets/jhuapl-bio/taxtriage
userName : eriny
profile : docker
configFiles : /home/eriny/.nextflow/assets/jhuapl-bio/taxtriage/nextflow.config
Input/output options (Required)
input : samplesheet.csv
db : /Volumes/IDGenomics_NAS/Data/kraken2_db/2023-06-05
outdir : taxtriage
Preliminary and QC
trim : null
Metagenomics Parameters
top_per_taxa : 10239:20:S 2:20:S
low_memory : null
download_db : null
top_hits_count : 3
Skip Steps
skip_fastp : null
skip_krona : null
skip_assembly : false
!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/taxtriage for your analysis please cite:
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/taxtriage/blob/master/CITATIONS.md
------------------------------------------------------
Min Quality set to default
No assembly file given, downloading the standard ncbi one
executor > local (4)
[e7/6e1678] process > NFCORE_TAXTRIAGE:TAXTRIAGE:DOWNLOAD_TAXTAB [100%] 1 of 1, cached: 1 ✔
[65/bb7f0c] process > NFCORE_TAXTRIAGE:TAXTRIAGE:GET_ASSEMBLIES [100%] 1 of 1, cached: 1 ✔
[f2/130c91] process > NFCORE_TAXTRIAGE:TAXTRIAGE:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv) [100%] 1 of 1, cached: 1 ✔
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ARTIC_GUPPYPLEX -
executor > local (4)
[e7/6e1678] process > NFCORE_TAXTRIAGE:TAXTRIAGE:DOWNLOAD_TAXTAB [100%] 1 of 1, cached: 1 ✔
[65/bb7f0c] process > NFCORE_TAXTRIAGE:TAXTRIAGE:GET_ASSEMBLIES [100%] 1 of 1, cached: 1 ✔
[f2/130c91] process > NFCORE_TAXTRIAGE:TAXTRIAGE:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv) [100%] 1 of 1, cached: 1 ✔
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ARTIC_GUPPYPLEX -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:PYCOQC -
[2c/b16ec9] process > NFCORE_TAXTRIAGE:TAXTRIAGE:FASTP (sample58) [ 50%] 1 of 2, cached: 1
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:FASTQC -
[c4/92d15c] process > NFCORE_TAXTRIAGE:TAXTRIAGE:NANOPLOT (sample59) [ 0%] 0 of 1
[cf/8e4406] process > NFCORE_TAXTRIAGE:TAXTRIAGE:KRAKEN2_KRAKEN2 (sample59) [100%] 1 of 1, cached: 1
[14/431c7d] process > NFCORE_TAXTRIAGE:TAXTRIAGE:VISUALIZE_REPORTS:KRONA_KTIMPORTTAXONOMY (sample59) [100%] 1 of 1, cached: 1
[ff/451b54] process > NFCORE_TAXTRIAGE:TAXTRIAGE:TOP_HITS (sample59) [100%] 1 of 1
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:MERGEDKRAKENREPORT -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:FILTERKRAKEN -
[bf/d7e555] process > NFCORE_TAXTRIAGE:TAXTRIAGE:DOWNLOAD_ASSEMBLY (sample59) [100%] 1 of 1
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:SAMTOOLS_FAIDX [ 0%] 0 of 1
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BOWTIE2_BUILD -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BOWTIE2_ALIGN -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:MINIMAP2_ALIGN [ 0%] 0 of 1
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:SAMTOOLS_DEPTH -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:SAMTOOLS_INDEX -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:SAMTOOLS_COVERAGE -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BCFTOOLS_MPILEUP_OXFORD -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BCFTOOLS_MPILEUP_ILLUMINA -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:SPLIT_VCF -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BCFTOOLS_INDEX -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BCFTOOLS_STATS -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BCFTOOLS_CONSENSUS -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:RSEQC_BAMSTAT -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:CONFIDENCE_METRIC -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:CONVERT_CONFIDENCE -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:MERGE_CONFIDENCE -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:SPADES_ILLUMINA -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:FLYE -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:CUSTOM_DUMPSOFTWAREVERSIONS -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:MULTIQC -
empty
____________________________
ERROR ~ Invalid method invocation `call` with arguments: [[id:sample59, single_end:true, platform:OXFORD, fastq_1:combined/sample59.fastq.gz, fastq_2:, trim:true, directory:false, sequencing_summary:null], /Volumes/BioNGS_1/UT-P2S01293-231116/UT-P2S01293-231116/20231116_2158_P2S-01293-B_PAS24124_ea91207e/work/ff/451b540cf89c2bacdfed8f5a6dd04c/sample59.top_report.tsv, [/Volumes/BioNGS_1/UT-P2S01293-231116/UT-P2S01293-231116/20231116_2158_P2S-01293-B_PAS24124_ea91207e/work/cf/8e4406123342809d8386958621d9ec/sample59.classified.fastq.gz], /Volumes/BioNGS_1/UT-P2S01293-231116/UT-P2S01293-231116/20231116_2158_P2S-01293-B_PAS24124_ea91207e/work/bf/d7e555e2341287907a3e7296aa14d6/sample59.output.references.fasta] (java.util.ArrayList) on _closure24 type
-- Check '.nextflow.log' file for details
I decided to skip fastp, and I HAVE A NEW ERROR!
This time it's due to the "label 'process_extreme'" for Kraken2. This requires Kraken2 to fail because our 5 year old system doesn't have enough memory. Is there a reason you'd like that as the default setting? I know how to change it in a config file (which I'll try sometime ... eventually), but if this workflow is expected to use those kinds of resources I need to order a new linux workstation.
$ nextflow run jhuapl-bio/taxtriage --input samplesheet.csv --outdir taxtriage -profile docker -resume --db /Volumes/IDGenomics_NAS/Data/kraken2_db/2023-06-05 -r main --skip_assembly false --top_hits_count 3 --skip_fastp -with-tower
N E X T F L O W ~ version 23.10.0
Launching `https://github.com/jhuapl-bio/taxtriage` [nasty_koch] DSL2 - revision: a603a52746 [main]
WARN: Found unexpected parameters:
* --max_time: 240.h
* --max_cpus: 16
* --max_memory: 1380.GB
* --config_profile_name: null
* --config_profile_url: null
* --config_profile_contact: null
* --config_profile_description: null
* --custom_config_base: https://raw.githubusercontent.com/nf-core/configs/master
* --custom_config_version: master
* --enable_conda: false
* --show_hidden_params: false
* --validate_params: true
* --help: false
* --monochrome_logs: false
* --plaintext_email: false
* --email_on_fail: null
* --publish_dir_mode: copy
* --tracedir: taxtriage/pipeline_info
* --max_multiqc_email_size: 25.MB
* --multiqc_logo: null
* --skip_variants: null
* --skip_consensus: null
* --subsample: null
* --top_hits_counts: null
* --minq: null
* --three_prime_clip_r2: null
* --three_prime_clip_r1: null
* --clip_r1: null
* --clip_r2: null
* --spades_hmm: null
* --remove_reference_file: null
- Ignore this warning: params.schema_ignore_params = "max_time,max_cpus,max_memory,config_profile_name,config_profile_url,config_profile_contact,config_profile_description,custom_config_base,custom_config_version,enable_conda,show_hidden_params,validate_params,help,monochrome_logs,plaintext_email,email_on_fail,publish_dir_mode,tracedir,max_multiqc_email_size,multiqc_logo,skip_variants,skip_consensus,subsample,top_hits_counts,minq,three_prime_clip_r2,three_prime_clip_r1,clip_r1,clip_r2,spades_hmm,remove_reference_file"
------------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/taxtriage v1.0dev
------------------------------------------------------
Core Nextflow options
revision : main
runName : nasty_koch
containerEngine: docker
launchDir : /Volumes/BioNGS_1/UT-P2S01293-231116/UT-P2S01293-231116/20231116_2158_P2S-01293-B_PAS24124_ea91207e
workDir : /Volumes/BioNGS_1/UT-P2S01293-231116/UT-P2S01293-231116/20231116_2158_P2S-01293-B_PAS24124_ea91207e/work
projectDir : /home/eriny/.nextflow/assets/jhuapl-bio/taxtriage
userName : eriny
profile : docker
configFiles : /home/eriny/.nextflow/assets/jhuapl-bio/taxtriage/nextflow.config
Input/output options (Required)
input : samplesheet.csv
db : /Volumes/IDGenomics_NAS/Data/kraken2_db/2023-06-05
outdir : taxtriage
Preliminary and QC
trim : null
Metagenomics Parameters
top_per_taxa : 10239:20:S 2:20:S
low_memory : null
download_db : null
top_hits_count : 3
Skip Steps
skip_fastp : true
skip_krona : null
skip_assembly : false
!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/taxtriage for your analysis please cite:
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/taxtriage/blob/master/CITATIONS.md
------------------------------------------------------
Min Quality set to default
No assembly file given, downloading the standard ncbi one
Monitor the execution with Nextflow Tower using this URL: https://tower.nf/user/erin-olde/watch/phFeV0ahxZm6Y
executor > local (2)
[e7/6e1678] process > NFCORE_TAXTRIAGE:TAXTRIAGE:DOWNLOAD_TAXTAB [100%] 1 of 1, cached: 1 ✔
[65/bb7f0c] process > NFCORE_TAXTRIAGE:TAXTRIAGE:GET_ASSEMBLIES [100%] 1 of 1, cached: 1 ✔
[f2/130c91] process > NFCORE_TAXTRIAGE:TAXTRIAGE:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv) [100%] 1 of 1, cached: 1 ✔
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ARTIC_GUPPYPLEX -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:PYCOQC -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:FASTQC -
[52/7b6ec1] process > NFCORE_TAXTRIAGE:TAXTRIAGE:NANOPLOT (sample58) [ 0%] 0 of 2
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:KRAKEN2_KRAKEN2 [ 0%] 0 of 2
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:VISUALIZE_REPORTS:KRONA_KTIMPORTTAXONOMY -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:TOP_HITS -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:MERGEDKRAKENREPORT -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:FILTERKRAKEN -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:DOWNLOAD_ASSEMBLY -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:SAMTOOLS_FAIDX -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BOWTIE2_BUILD -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BOWTIE2_ALIGN -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:MINIMAP2_ALIGN -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:SAMTOOLS_DEPTH -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:SAMTOOLS_INDEX -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:SAMTOOLS_COVERAGE -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BCFTOOLS_MPILEUP_OXFORD -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BCFTOOLS_MPILEUP_ILLUMINA -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:SPLIT_VCF -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BCFTOOLS_INDEX -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BCFTOOLS_STATS -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BCFTOOLS_CONSENSUS -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:RSEQC_BAMSTAT -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:CONFIDENCE_METRIC -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:CONVERT_CONFIDENCE -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:MERGE_CONFIDENCE -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:SPADES_ILLUMINA -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:FLYE -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:CUSTOM_DUMPSOFTWAREVERSIONS -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:MULTIQC -
empty
____________________________
Monitor the execution with Nextflow Tower using this URL: https://tower.nf/user/erin-olde/watch/phFeV0ahxZm6Y
executor > local (2)
[e7/6e1678] process > NFCORE_TAXTRIAGE:TAXTRIAGE:DOWNLOAD_TAXTAB [100%] 1 of 1, cached: 1 ✔
[65/bb7f0c] process > NFCORE_TAXTRIAGE:TAXTRIAGE:GET_ASSEMBLIES [100%] 1 of 1, cached: 1 ✔
[f2/130c91] process > NFCORE_TAXTRIAGE:TAXTRIAGE:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv) [100%] 1 of 1, cached: 1 ✔
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ARTIC_GUPPYPLEX -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:PYCOQC -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:FASTQC -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:NANOPLOT (sample58) -
[bd/bf11b8] process > NFCORE_TAXTRIAGE:TAXTRIAGE:KRAKEN2_KRAKEN2 (sample58) [ 50%] 1 of 2, failed: 1
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:VISUALIZE_REPORTS:KRONA_KTIMPORTTAXONOMY -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:TOP_HITS -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:MERGEDKRAKENREPORT -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:FILTERKRAKEN -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:DOWNLOAD_ASSEMBLY -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:SAMTOOLS_FAIDX -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BOWTIE2_BUILD -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BOWTIE2_ALIGN -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:MINIMAP2_ALIGN -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:SAMTOOLS_DEPTH -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:SAMTOOLS_INDEX -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:SAMTOOLS_COVERAGE -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BCFTOOLS_MPILEUP_OXFORD -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BCFTOOLS_MPILEUP_ILLUMINA -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:SPLIT_VCF -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BCFTOOLS_INDEX -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BCFTOOLS_STATS -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BCFTOOLS_CONSENSUS -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:RSEQC_BAMSTAT -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:CONFIDENCE_METRIC -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:CONVERT_CONFIDENCE -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:MERGE_CONFIDENCE -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:SPADES_ILLUMINA -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:FLYE -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:CUSTOM_DUMPSOFTWAREVERSIONS -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:MULTIQC -
empty
____________________________
ERROR ~ Error executing process > 'NFCORE_TAXTRIAGE:TAXTRIAGE:KRAKEN2_KRAKEN2 (sample58)'
Caused by:
Process requirement exceeds available memory -- req: 825 GB; avail: 503.3 GB
Command executed:
kraken2 \
--db 2023-06-05 \
--threads 10 \
--report sample58.kraken2.report.txt \
--gzip-compressed \
--unclassified-out sample58.unclassified.fastq \
--classified-out sample58.classified.fastq \
--output sample58.kraken2.classifiedreads.txt \
\
\
sample58.fastq.gz
pigz -p 10 *.fastq
cat <<-END_VERSIONS > versions.yml
"NFCORE_TAXTRIAGE:TAXTRIAGE:KRAKEN2_KRAKEN2":
kraken2: $(echo $(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*$//')
pigz: $( pigz --version 2>&1 | sed 's/pigz //g' )
END_VERSIONS
Command exit status:
-
Command output:
(empty)
Work dir:
/Volumes/BioNGS_1/UT-P2S01293-231116/UT-P2S01293-231116/20231116_2158_P2S-01293-B_PAS24124_ea91207e/work/bd/bf11b81663bdceee10178383da43b9
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
@erinyoung if you're working on the main branch that is the case. We had tailored that for running the nt database on NF Tower but I've reverted it back to just "suphigh" memory as it was before
Description of the bug
I likely didn't create the sample sheet correctly or use the correct options. Sorry! I've attached the .nextflow.log as well as my sample sheet.
I ran the taxtriage test profile, and that worked okay. I decided to use it on "real" samples. They are two metagenomic samples from milk. The workflow was running until it wasn't.
Command used and terminal output
Relevant files
This is the .nextflow.log file: nextflow.log
And my sample sheet: samplesheet.csv
System information
N E X T F L O W version 23.10.0 build 5889 Hardware : Local Executor : local Container engine: Docker OS : CentOS Version of jhuapl-bio/taxtriage : current version (pulled 11/22/2023)