Offending keys error when running nf-core sarek on ~500 samples

[acjmmartin]

Bug report

Expected behavior and actual behavior

In the mapping step of nf-core sarek, fastqs should be aligned to a reference genome. This works perfectly with a subset of my sample sheet (25 samples) but when running the complete sample sheet (497 samples) I get a "offending keys" error message. There are no duplicates in the sample sheet and none of the input files are missing.

Steps to reproduce the problem

I used to following commands: nextflow run /camp/project/tracerX/working/PIPELINES/nf-core/sarek/2.7/workflow -profile crick --step mapping --genome GRCh37 --input /camp/project/tracerX/working/CRENAL/WORKING/Tx200/clean_scripts/sex_sheet_Tx200_v6_SampleSheet_sarek.tsv --target_bed /camp/project/tracerX/working/PIPELINES/nf-core/sarek/2.7/custom_references/bed_files/No_chr_Rabbit_Hole_v6.bed --outdir /camp/project/tracerX/working/CRENAL/OUTPUT/Tx200_clean -c /camp/project/tracerX/working/PIPELINES/nf-core/sarek/2.7/custom_configs/custom_crick_sarek_hp.config

Program output

Error executing process > 'MapReads (K648-L003)'

Caused by:
  Oops.. something wrong happened while creating task 'MapReads' unique id -- Offending keys: [
 - type=java.util.UUID value=cf7e96ff-2ac4-4cd8-9ccc-e2c35c5a04e3, 
 - type=java.lang.String value=MapReads, 
 - type=java.lang.String value=CN = params.sequencing_center ? "CN:${params.sequencing_center}\\t" : ""
readGroup = "@RG\\tID:${idRun}\\t${CN}PU:${idRun}\\tSM:${idSample}\\tLB:${idSample}\\tPL:illumina"
status = statusMap[idPatient, idSample]
extra = status == 1 ? "-B 3" : ""
convertToFastq = hasExtension(inputFile1, "bam") ? "gatk --java-options -Xmx${task.memory.toGiga()}g SamToFastq --INPUT=${inputFile1} --FASTQ=/dev/stdout --INTERLEAVE=true --NON_PF=true | \\" : ""
input = hasExtension(inputFile1, "bam") ? "-p /dev/stdin - 2> >(tee ${inputFile1}.bwa.stderr.log >&2)" : "${inputFile1} ${inputFile2}"
aligner = params.aligner == "bwa-mem2" ? "bwa-mem2" : "bwa"
"""
    ${convertToFastq}
    ${aligner} mem -K 100000000 -R \"${readGroup}\" ${extra} -t ${task.cpus} -M ${fasta} \
    ${input} | \
    samtools sort --threads ${task.cpus} -m 2G - > ${idSample}_${idRun}.bam
    """
, 
 - type=java.lang.String value=/camp/project/tracerX/working/PIPELINES/nf-core/sarek/2.7/workflow/../singularity-images/nfcore-sarek-2.7.img, 
 - type=java.lang.String value=idPatient, 
 - type=java.lang.String value=K648, 
 - type=java.lang.String value=idSample, 
 - type=java.lang.String value=G_K648_BC1d1, 
 - type=java.lang.String value=idRun, 
 - type=java.lang.String value=L003, 
 - type=java.lang.String value=inputFile1, 
 - type=nextflow.util.ArrayBag value=[FileHolder(sourceObj:/camp/project/tracerX/working/CRENAL/SOURCES/Tx200_panel_v6/AUY227A265_S57_L003_R1_001.fastq.gz, storePath:/camp/stp/sequencing/inputs/instruments/fastq/190710_NB501505_0101_AH5YHKBGXB/fastq/DN18127/AUY227A265_S57_L003_R1_001.fastq.gz, stageName:AUY227A265_S57_L003_R1_001.fastq.gz)], 
 - type=java.lang.String value=inputFile2, 
 - type=nextflow.util.ArrayBag value=[FileHolder(sourceObj:/camp/project/tracerX/working/CRENAL/SOURCES/Tx200_panel_v6/AUY227A265_S57_L003_R2_001.fastq.gz, storePath:/camp/stp/sequencing/inputs/instruments/fastq/190710_NB501505_0101_AH5YHKBGXB/fastq/DN18127/AUY227A265_S57_L003_R2_001.fastq.gz, stageName:AUY227A265_S57_L003_R2_001.fastq.gz)], 
 - type=java.lang.String value=bwaIndex, 
 - type=nextflow.util.ArrayBag value=[FileHolder(sourceObj:/camp/svc/reference/Genomics/aws-igenomes/Homo_sapiens/GATK/GRCh37/Sequence/BWAIndex/human_g1k_v37_decoy.fasta.ann, storePath:/camp/svc/reference/Genomics/aws-igenomes/Homo_sapiens/GATK/GRCh37/Sequence/BWAIndex/human_g1k_v37_decoy.fasta.ann, stageName:human_g1k_v37_decoy.fasta.ann), FileHolder(sourceObj:/camp/svc/reference/Genomics/aws-igenomes/Homo_sapiens/GATK/GRCh37/Sequence/BWAIndex/human_g1k_v37_decoy.fasta.pac, storePath:/camp/svc/reference/Genomics/aws-igenomes/Homo_sapiens/GATK/GRCh37/Sequence/BWAIndex/human_g1k_v37_decoy.fasta.pac, stageName:human_g1k_v37_decoy.fasta.pac), FileHolder(sourceObj:/camp/svc/reference/Genomics/aws-igenomes/Homo_sapiens/GATK/GRCh37/Sequence/BWAIndex/human_g1k_v37_decoy.fasta.sa, storePath:/camp/svc/reference/Genomics/aws-igenomes/Homo_sapiens/GATK/GRCh37/Sequence/BWAIndex/human_g1k_v37_decoy.fasta.sa, stageName:human_g1k_v37_decoy.fasta.sa), FileHolder(sourceObj:/camp/svc/reference/Genomics/aws-igenomes/Homo_sapiens/GATK/GRCh37/Sequence/BWAIndex/human_g1k_v37_decoy.fasta.bwt, storePath:/camp/svc/reference/Genomics/aws-igenomes/Homo_sapiens/GATK/GRCh37/Sequence/BWAIndex/human_g1k_v37_decoy.fasta.bwt, stageName:human_g1k_v37_decoy.fasta.bwt), FileHolder(sourceObj:/camp/svc/reference/Genomics/aws-igenomes/Homo_sapiens/GATK/GRCh37/Sequence/BWAIndex/human_g1k_v37_decoy.fasta.amb, storePath:/camp/svc/reference/Genomics/aws-igenomes/Homo_sapiens/GATK/GRCh37/Sequence/BWAIndex/human_g1k_v37_decoy.fasta.amb, stageName:human_g1k_v37_decoy.fasta.amb)], 
 - type=java.lang.String value=fasta, 
 - type=nextflow.util.ArrayBag value=[FileHolder(sourceObj:/camp/svc/reference/Genomics/aws-igenomes/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta, storePath:/camp/svc/reference/Genomics/aws-igenomes/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta, stageName:human_g1k_v37_decoy.fasta)], 
 - type=java.lang.String value=fastaFai, 
 - type=nextflow.util.ArrayBag value=[FileHolder(sourceObj:/camp/svc/reference/Genomics/aws-igenomes/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta.fai, storePath:/camp/svc/reference/Genomics/aws-igenomes/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta.fai, stageName:human_g1k_v37_decoy.fasta.fai)], 
 - type=java.lang.String value=$, 
 - type=java.lang.Boolean value=true, 
 - type=java.util.HashMap$EntrySet value=[params.aligner=bwa-mem, statusMap={[K656, G_K656_BC1d1]=0, [K656, G_K656_R1d1]=1, etc }, params.sequencing_center=null]]`

Environment

• Nextflow version: 21.04.0
• Java version: 11.0.2
• Operating system: Linux
• Bash version: GNU bash, version 4.2.46(2)-release (x86_64-redhat-linux-gnu)

Additional context

nextflow.log

[abhi18av]

Hi @acjmmartin ,

Perhaps this should be reported to nf-core/sarek repo? Or the #sarek slack channel?

[acjmmartin]

Hi @abhi18av , I raised the issue with them and they advised me to raise it here because the only exception they could find in the nextflow log was a ["ConcurrentModificationException"

[abhi18av]

Ah, I see.

Possible for you to try again after doing a nextflow self-update (to update to v21.10.6 release) and then appending -resume to your command?

If this fails again, please share the .nextflow.log file

[b97pla]

I'm having the same problem using v21.10.6, were you able to get to the bottom of this issue @acjmmartin ?

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[acjmmartin]

I'm having the same problem using v21.10.6, were you able to get to the bottom of this issue @acjmmartin ?

Apologies, I moved on to a different project so never got to the bottom of this issue. Have you? @b97pla

[acjmmartin]

The issue disappeared when using Nextflow/22.04.0