atacseq
atacseq copied to clipboard
Reduce available memory for Picard Mark Duplicates
Right now, the pipeline fails for me with the following error:
Error executing process > 'NFCORE_ATACSEQ:ATACSEQ:MERGED_LIBRARY_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (DMSO_REP4)'
Caused by:
Process `NFCORE_ATACSEQ:ATACSEQ:MERGED_LIBRARY_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (DMSO_REP4)` terminated with an error exit status (1)
Command executed:
picard \
-Xmx36g \
MarkDuplicates \
--ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp \
--INPUT DMSO_REP4.mLb.sorted.bam \
--OUTPUT DMSO_REP4.mLb.mkD.sorted.bam \
--REFERENCE_SEQUENCE genome.fa \
--METRICS_FILE DMSO_REP4.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 exit status:
1
Command output:
Error occurred during initialization of VM
Could not reserve enough space for 37748736KB object heap
I ran into this issue with the cutandrun pipeline and the rnaseq pipeline. In both cases, the fix was to allocate only a fraction of the available memory when launching the process. Here is the relevant change in the cutandrun pipeline. Thanks @drpatelh for the change in the cutandrun repo.
PR checklist
- [x] This comment contains a description of changes (with reason).
- [ ] If you've fixed a bug or added code that should be tested, add tests!
- [ ] If you've added a new tool - have you followed the pipeline conventions in the contribution docs- [ ] If necessary, also make a PR on the nf-core/atacseq branch on the nf-core/test-datasets repository.
- [ ] Make sure your code lints (
nf-core lint
). - [ ] Ensure the test suite passes (
nextflow run . -profile test,docker --outdir <OUTDIR>
). - [ ] Usage Documentation in
docs/usage.md
is updated. - [ ] Output Documentation in
docs/output.md
is updated. - [ ]
CHANGELOG.md
is updated. - [ ]
README.md
is updated (including new tool citations and authors/contributors).