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Description
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
Line 358 in 1a1dbe5
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_DIRRelevant 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
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