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Missing output file(s) `clair_output/tmp/CHUNK_LIST` expected by process `snp:make_chunks (1)` #190

Open nikelau opened 3 weeks ago

nikelau commented 3 weeks ago

Operating System

Windows 11

Other Linux

No response

Workflow Version

2.2.3

Workflow Execution

EPI2ME Desktop (Local)

Other workflow execution

No response

EPI2ME Version

EPI2ME V5.1.14

CLI command run

No response

Workflow Execution - CLI Execution Profile

None

What happened?

I am running the new human variation workflow 2.2.3 on some old data and this seemed to have happened on one of my two windows PCs working on the same input data. Any insights on why this happens only on one PC only? The other seemed to have worked through this step without error.

Thanks!

Relevant log output

--------------------------------------------------------------------------------
This is epi2me-labs/wf-human-variation v2.2.3.
--------------------------------------------------------------------------------
Searching input for [.bam, .ubam] files.
[c5/1d40b0] Submitted process > sv:runReport:getVersions
[d6/7dd2f4] Submitted process > cnv_spectre:getParams
[48/c2924b] Submitted process > report_snp:getVersions
[0a/dd1d06] Submitted process > sv:runReport:getParams
[db/fda996] Submitted process > str:getParams
[e8/ef4952] Submitted process > getVersions
[18/9e0ab1] Submitted process > cnv_spectre:getVersions
[a6/598379] Submitted process > getParams
[9c/405c53] Submitted process > str:getVersions
[1a/53b7b1] Submitted process > report_snp:getParams
[90/de37f5] Submitted process > cram_cache (1)
[15/5e928e] Submitted process > ingress:checkBamHeaders (1)
[52/311c90] Submitted process > cnv_spectre:add_snp_tools_to_versions
[bf/ee173e] Submitted process > ingress:catSortBams (1)
[f7/e831dc] Submitted process > getAllChromosomesBed (1)
[35/c28e71] Submitted process > ingress:check_for_alignment (1)
[ae/4470bb] Submitted process > ingress:minimap2_alignment (1)
[a5/cd06af] Submitted process > lookup_clair3_model (1)
[27/f1d750] Submitted process > validate_modbam (1)
[b4/2f7935] Submitted process > readStats (1)
[83/aa808c] Submitted process > mosdepth_input (1)
[56/9e1670] Submitted process > cnv_spectre:mosdepth (1)
[7c/fc7bff] Submitted process > getGenome (1)
Autoselected Clair3 model: r941_prom_sup_g5014
[f1/c8a2d1] Submitted process > snp:make_chunks (1)
[dc/6aeff9] Submitted process > sample_probs (1)
ERROR ~ Error executing process > 'snp:make_chunks (1)'
Caused by:
  Missing output file(s) `clair_output/tmp/CHUNK_LIST` expected by process `snp:make_chunks (1)`
Command executed:
  # CW-2456: save command line to add to VCF file (very long command...)
  mkdir -p clair_output/tmp
  echo "run_clair3.sh --bam_fn=SAMPLE.cram  --ref_fn=hg38.analysisSet.fa  --output=clair_output --platform=ont --sample_name=SAMPLE --model_path=model --ctg_name=null --ctg_name chr1,1,chr2,2,chr3,3,chr4,4,chr5,5,chr6,6,chr7,7,chr8,8,chr9,9,chr10,10,chr11,11,chr12,12,chr13,13,chr14,14,chr15,15,chr16,16,chr17,17,chr18,18,chr19,19,chr20,20,chr21,21,chr22,22,chrX,X,chrY,Y,chrM,M,chrMT,MT --include_all_ctgs=false --chunk_num=0 --chunk_size=5000000 --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --snp_min_af 0.08 --indel_min_af 0.15 --min_contig_size=0" > clair_output/tmp/CMD
  # CW-2456: prepare other inputs normally
  python $(which clair3.py) CheckEnvs             --bam_fn SAMPLE.cram                          --output_fn_prefix clair_output             --ref_fn hg38.analysisSet.fa                          --ctg_name chr1,1,chr2,2,chr3,3,chr4,4,chr5,5,chr6,6,chr7,7,chr8,8,chr9,9,chr10,10,chr11,11,chr12,12,chr13,13,chr14,14,chr15,15,chr16,16,chr17,17,chr18,18,chr19,19,chr20,20,chr21,21,chr22,22,chrX,X,chrY,Y,chrM,M,chrMT,MT             --chunk_num 0             --chunk_size 5000000             --include_all_ctgs false             --threads 1              --qual 2             --sampleName SAMPLE             --var_pct_full 0.7             --ref_pct_full 0.1             --snp_min_af 0.08             --indel_min_af 0.15             --min_contig_size 0             --cmd_fn clair_output/tmp/CMD
Command exit status:
  0
Command output:
  [WARNING] Contig name chr5 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name chr6 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name chr7 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name chr8 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name chr9 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name chr10 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name chr11 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name chr12 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name chr13 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name chr14 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name chr15 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name chr16 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name chr17 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name chr18 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name chr19 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name chr20 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name chr21 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name chr22 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name chrX provided but no mapped reads in BAM, skip!
  [WARNING] Contig name chrY provided but no mapped reads in BAM, skip!
  [WARNING] Contig name 1 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name 2 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name 3 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name 4 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name 5 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name 6 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name 7 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name 8 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name 9 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name 10 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name 11 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name 12 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name 13 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name 14 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name 15 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name 16 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name 17 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name 18 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name 19 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name 20 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name 21 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name 22 provided but no mapped reads in BAM, skip!
  [WARNING] Contig name X provided but no mapped reads in BAM, skip!
  [WARNING] Contig name Y provided but no mapped reads in BAM, skip!
  [WARNING] Contig name chrMT provided but no mapped reads in BAM, skip!
  [WARNING] Contig name M provided but no mapped reads in BAM, skip!
  [WARNING] Contig name MT provided but no mapped reads in BAM, skip!
  [WARNING] Contig name chrM provided but no mapped reads in BAM, skip!
  [WARNING] No mapped reads support in BAM for provided contigs set chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y chrMT M MT chrM
  [WARNING] No contig intersection found, output header only in clair_output/merge_output.vcf.gz
Command error:
  [INFO] Create folder clair_output/log
  [INFO] Create folder clair_output/tmp/pileup_output
  [INFO] Create folder clair_output/tmp/merge_output
  [INFO] Create folder clair_output/tmp/phase_output
  [INFO] Create folder clair_output/tmp/gvcf_tmp_output
  [INFO] Create folder clair_output/tmp/full_alignment_output
  [INFO] Create folder clair_output/tmp/phase_output/phase_vcf
  [INFO] Create folder clair_output/tmp/phase_output/phase_bam
  [INFO] Create folder clair_output/tmp/full_alignment_output/candidate_bed
  Usage: samtools idxstats [options] <in.bam>
        --input-fmt-option OPT[=VAL]
                 Specify a single input file format option in the form
                 of OPTION or OPTION=VALUE
    -@, --threads INT
                 Number of additional threads to use [0]
        --verbosity INT
                 Set level of verbosity
Work dir:
  /mnt/c/Users/genetics-user/Desktop/Nanopore files/instances/wf-human-variation_01HZNQ0FJPJKAV1ZAMQF62JN2H/work/f1/c8a2d1db9b1eeb227e357eef480ec5
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
 -- Check '/mnt/c/Users/genetics-user/Desktop/Nanopore files/instances/wf-human-variation_01HZNQ0FJPJKAV1ZAMQF62JN2H/nextflow.log' file for details
WARN: Killing running tasks (4)

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

yes

Other demo data information

No response

SamStudio8 commented 3 weeks ago

Would you kindly post your entire .nextflow.log related to this workflow instance to help us reconstruct the order of workflow operations

On Thu, 6 Jun 2024, 06:54 nikelau, @.***> wrote:

Operating System

Windows 11 Other Linux

No response Workflow Version

2.2.3 Workflow Execution

EPI2ME Desktop (Local) Other workflow execution

No response EPI2ME Version

EPI2ME V5.1.14 CLI command run

No response Workflow Execution - CLI Execution Profile

None What happened?

I am running the new human variation workflow 2.2.3 on some old data and this seemed to have happened on one of my two windows PCs working on the same input data. Any insights on why this happens only on one PC only? The other seemed to have worked through this step without error.

Thanks! Relevant log output

This is epi2me-labs/wf-human-variation v2.2.3.

Searching input for [.bam, .ubam] files. [c5/1d40b0] Submitted process > sv:runReport:getVersions [d6/7dd2f4] Submitted process > cnv_spectre:getParams [48/c2924b] Submitted process > report_snp:getVersions [0a/dd1d06] Submitted process > sv:runReport:getParams [db/fda996] Submitted process > str:getParams [e8/ef4952] Submitted process > getVersions [18/9e0ab1] Submitted process > cnv_spectre:getVersions [a6/598379] Submitted process > getParams [9c/405c53] Submitted process > str:getVersions [1a/53b7b1] Submitted process > report_snp:getParams [90/de37f5] Submitted process > cram_cache (1) [15/5e928e] Submitted process > ingress:checkBamHeaders (1) [52/311c90] Submitted process > cnv_spectre:add_snp_tools_to_versions [bf/ee173e] Submitted process > ingress:catSortBams (1) [f7/e831dc] Submitted process > getAllChromosomesBed (1) [35/c28e71] Submitted process > ingress:check_for_alignment (1) [ae/4470bb] Submitted process > ingress:minimap2_alignment (1) [a5/cd06af] Submitted process > lookup_clair3_model (1) [27/f1d750] Submitted process > validate_modbam (1) [b4/2f7935] Submitted process > readStats (1) [83/aa808c] Submitted process > mosdepth_input (1) [56/9e1670] Submitted process > cnv_spectre:mosdepth (1) [7c/fc7bff] Submitted process > getGenome (1) Autoselected Clair3 model: r941_prom_sup_g5014 [f1/c8a2d1] Submitted process > snp:make_chunks (1) [dc/6aeff9] Submitted process > sample_probs (1) ERROR ~ Error executing process > 'snp:make_chunks (1)' Caused by: Missing output file(s) clair_output/tmp/CHUNK_LIST expected by process snp:make_chunks (1) Command executed:

CW-2456: save command line to add to VCF file (very long command...)

mkdir -p clair_output/tmp echo "run_clair3.sh --bam_fn=SAMPLE.cram --ref_fn=hg38.analysisSet.fa --output=clair_output --platform=ont --sample_name=SAMPLE --model_path=model --ctg_name=null --ctg_name chr1,1,chr2,2,chr3,3,chr4,4,chr5,5,chr6,6,chr7,7,chr8,8,chr9,9,chr10,10,chr11,11,chr12,12,chr13,13,chr14,14,chr15,15,chr16,16,chr17,17,chr18,18,chr19,19,chr20,20,chr21,21,chr22,22,chrX,X,chrY,Y,chrM,M,chrMT,MT --include_all_ctgs=false --chunk_num=0 --chunk_size=5000000 --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --snp_min_af 0.08 --indel_min_af 0.15 --min_contig_size=0" > clair_output/tmp/CMD

CW-2456: prepare other inputs normally

python $(which clair3.py) CheckEnvs --bam_fn SAMPLE.cram --output_fn_prefix clair_output --ref_fn hg38.analysisSet.fa --ctg_name chr1,1,chr2,2,chr3,3,chr4,4,chr5,5,chr6,6,chr7,7,chr8,8,chr9,9,chr10,10,chr11,11,chr12,12,chr13,13,chr14,14,chr15,15,chr16,16,chr17,17,chr18,18,chr19,19,chr20,20,chr21,21,chr22,22,chrX,X,chrY,Y,chrM,M,chrMT,MT --chunk_num 0 --chunk_size 5000000 --include_all_ctgs false --threads 1 --qual 2 --sampleName SAMPLE --var_pct_full 0.7 --ref_pct_full 0.1 --snp_min_af 0.08 --indel_min_af 0.15 --min_contig_size 0 --cmd_fn clair_output/tmp/CMD Command exit status: 0 Command output: [WARNING] Contig name chr5 provided but no mapped reads in BAM, skip! [WARNING] Contig name chr6 provided but no mapped reads in BAM, skip! [WARNING] Contig name chr7 provided but no mapped reads in BAM, skip! [WARNING] Contig name chr8 provided but no mapped reads in BAM, skip! [WARNING] Contig name chr9 provided but no mapped reads in BAM, skip! [WARNING] Contig name chr10 provided but no mapped reads in BAM, skip! [WARNING] Contig name chr11 provided but no mapped reads in BAM, skip! [WARNING] Contig name chr12 provided but no mapped reads in BAM, skip! [WARNING] Contig name chr13 provided but no mapped reads in BAM, skip! [WARNING] Contig name chr14 provided but no mapped reads in BAM, skip! [WARNING] Contig name chr15 provided but no mapped reads in BAM, skip! [WARNING] Contig name chr16 provided but no mapped reads in BAM, skip! [WARNING] Contig name chr17 provided but no mapped reads in BAM, skip! [WARNING] Contig name chr18 provided but no mapped reads in BAM, skip! [WARNING] Contig name chr19 provided but no mapped reads in BAM, skip! [WARNING] Contig name chr20 provided but no mapped reads in BAM, skip! [WARNING] Contig name chr21 provided but no mapped reads in BAM, skip! [WARNING] Contig name chr22 provided but no mapped reads in BAM, skip! [WARNING] Contig name chrX provided but no mapped reads in BAM, skip! [WARNING] Contig name chrY provided but no mapped reads in BAM, skip! [WARNING] Contig name 1 provided but no mapped reads in BAM, skip! [WARNING] Contig name 2 provided but no mapped reads in BAM, skip! [WARNING] Contig name 3 provided but no mapped reads in BAM, skip! [WARNING] Contig name 4 provided but no mapped reads in BAM, skip! [WARNING] Contig name 5 provided but no mapped reads in BAM, skip! [WARNING] Contig name 6 provided but no mapped reads in BAM, skip! [WARNING] Contig name 7 provided but no mapped reads in BAM, skip! [WARNING] Contig name 8 provided but no mapped reads in BAM, skip! [WARNING] Contig name 9 provided but no mapped reads in BAM, skip! [WARNING] Contig name 10 provided but no mapped reads in BAM, skip! [WARNING] Contig name 11 provided but no mapped reads in BAM, skip! [WARNING] Contig name 12 provided but no mapped reads in BAM, skip! [WARNING] Contig name 13 provided but no mapped reads in BAM, skip! [WARNING] Contig name 14 provided but no mapped reads in BAM, skip! [WARNING] Contig name 15 provided but no mapped reads in BAM, skip! [WARNING] Contig name 16 provided but no mapped reads in BAM, skip! [WARNING] Contig name 17 provided but no mapped reads in BAM, skip! [WARNING] Contig name 18 provided but no mapped reads in BAM, skip! [WARNING] Contig name 19 provided but no mapped reads in BAM, skip! [WARNING] Contig name 20 provided but no mapped reads in BAM, skip! [WARNING] Contig name 21 provided but no mapped reads in BAM, skip! [WARNING] Contig name 22 provided but no mapped reads in BAM, skip! [WARNING] Contig name X provided but no mapped reads in BAM, skip! [WARNING] Contig name Y provided but no mapped reads in BAM, skip! [WARNING] Contig name chrMT provided but no mapped reads in BAM, skip! [WARNING] Contig name M provided but no mapped reads in BAM, skip! [WARNING] Contig name MT provided but no mapped reads in BAM, skip! [WARNING] Contig name chrM provided but no mapped reads in BAM, skip! [WARNING] No mapped reads support in BAM for provided contigs set chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y chrMT M MT chrM [WARNING] No contig intersection found, output header only in clair_output/merge_output.vcf.gz Command error: [INFO] Create folder clair_output/log [INFO] Create folder clair_output/tmp/pileup_output [INFO] Create folder clair_output/tmp/merge_output [INFO] Create folder clair_output/tmp/phase_output [INFO] Create folder clair_output/tmp/gvcf_tmp_output [INFO] Create folder clair_output/tmp/full_alignment_output [INFO] Create folder clair_output/tmp/phase_output/phase_vcf [INFO] Create folder clair_output/tmp/phase_output/phase_bam [INFO] Create folder clair_output/tmp/full_alignment_output/candidate_bed Usage: samtools idxstats [options] --input-fmt-option OPT[=VAL] Specify a single input file format option in the form of OPTION or OPTION=VALUE -@, --threads INT Number of additional threads to use [0] --verbosity INT Set level of verbosity Work dir: /mnt/c/Users/genetics-user/Desktop/Nanopore files/instances/wf-human-variation_01HZNQ0FJPJKAV1ZAMQF62JN2H/work/f1/c8a2d1db9b1eeb227e357eef480ec5 Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out -- Check '/mnt/c/Users/genetics-user/Desktop/Nanopore files/instances/wf-human-variation_01HZNQ0FJPJKAV1ZAMQF62JN2H/nextflow.log' file for details WARN: Killing running tasks (4)

Application activity log entry

No response Were you able to successfully run the latest version of the workflow with the demo data?

yes Other demo data information

No response

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