Picard "--TMP_DIR" arguments are hardcoded

[vondoRishi]

Description of the bug

An error "No space left on device" occurred by process NFCORE_ATACSEQ:ATACSEQ:MERGED_LIBRARY_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (E145I_REP1). Possible reason "--TMP_DIR" arguments are hardcoded in modules.config (example

atacseq/conf/modules.config

Line 358 in 1a1dbe5

ext.args = '--ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp'

).

Caused by:
Process NFCORE_ATACSEQ:ATACSEQ:MERGED_LIBRARY_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (E145I_REP1) terminated with an error exit status (1)

Command executed:

picard \
    -Xmx29491M \
    MarkDuplicates \
    --ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp \
    --INPUT E145I_REP1.mLb.sorted.bam \
    --OUTPUT E145I_REP1.mLb.mkD.sorted.bam \
    --REFERENCE_SEQUENCE Mus_musculus.GRCm38.dna.primary_assembly.fa \
    --METRICS_FILE E145I_REP1.mLb.mkD.sorted.MarkDuplicates.metrics.txt

cat <<-END_VERSIONS > versions.yml
"NFCORE_ATACSEQ:ATACSEQ:MERGED_LIBRARY_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES":
    picard: $(echo $(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS

Command error:

Runtime.totalMemory()=4311744512
  To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
  Exception in thread "main" htsjdk.samtools.SAMException: Error loading new map from disk.
        at htsjdk.samtools.CoordinateSortedPairInfoMap.ensureSequenceLoaded(CoordinateSortedPairInfoMap.java:143)
        at htsjdk.samtools.CoordinateSortedPairInfoMap.remove(CoordinateSortedPairInfoMap.java:86)
        at picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap.remove(DiskBasedReadEndsForMarkDuplicatesMap.java:61)
        at picard.sam.markduplicates.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:560)
        at picard.sam.markduplicates.MarkDuplicates.doWork(MarkDuplicates.java:270)
        at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:289)
        at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:104)
        at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:114)
  Caused by: java.io.IOException: No space left on device
        at java.base/java.io.FileOutputStream.writeBytes(Native Method)
        at java.base/java.io.FileOutputStream.write(FileOutputStream.java:349)
        at java.base/java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:81)
        at java.base/java.io.BufferedOutputStream.flush(BufferedOutputStream.java:142)
        at java.base/java.io.FilterOutputStream.close(FilterOutputStream.java:182)
        at htsjdk.samtools.CoordinateSortedPairInfoMap.ensureSequenceLoaded(CoordinateSortedPairInfoMap.java:119)

Command used and terminal output

Slurm declaration

export TMPDIR=$PWD
export SINGULARITY_TMPDIR=$PWD
export SINGULARITY_CACHEDIR=$PWD
unset XDG_RUNTIME_DIR

Relevant files

No response

System information

• Nextflow version - 24.01.0-edge
• Hardware - HPC
• Executor - slurm
• Container engine: - Singularity
• OS - Linux
• Version of nf-core/atacseq 2.1.2