Comments (3)
In case you use Docker, one workaround might be to limit the CPU resources of docker using --cpus=<value>
(https://docs.docker.com/config/containers/resource_constraints/#cpu)
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Apparently its not really effective to change that option: broadinstitute/picard#1223
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If that happens again - please re-open, as these changes are not 100% sure to fix the issue.
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Related Issues (20)
- Improve/add UMI deduplication metrics HOT 3
- Validate FASTQs prior to running pipeline
- --limitGenomeGenerateRAM
- --additional_fasta gene.fa parameter adds fasta but final gene is not present in the final count matrix HOT 4
- Pipe line Error with HiSAT2 Aligner HOT 3
- Symlink issue in NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TX2GENE HOT 5
- Replace nf-validation with nf-schema
- NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN: failed with exit status 140 and 102 HOT 5
- NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN_IGENOMES Segmentation fault HOT 16
- Command not found HOT 2
- QUALIMAP_RNASEQ error simultaneous access on same dir HOT 10
- Pipeline gets stuck with weird nextflow.log HOT 4
- Please add gene names to merged rsem output files
- SAMException: Sequence name [...] doesn't match regex then fails HOT 1
- MultiQC report is missing fastQC results on the dev branch HOT 11
- Dog seems unsupported, first issue is igenomes reference fasta dir vs RNAseq regex HOT 5
- GUNZIP does not work for relative paths specified with --fasta and --gtf HOT 1
- External Argument Documentation HOT 3
- Error running process `NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION`
- pipeline no longer compatible with newest STAR 2.7.11b
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