Comments (2)
Additional suggestion to increase the RAM allocated for this process, e.g.
process {
withName: 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK' {
memory = 200.GB
}
}
Could work with less than 200, just haven't tried it.
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I have been running jobs using the attached workflow, and one of my workflows has been struggling to finish as it continues to encounter this error due to there being many samples to analyze. This study with 45 samples hasn't successfully finished the differential abundance pipeline, depite having 256 GBs of memory and 64 CPUs per task when running on an HPC. I've run jobs that have anywhere from 5 to 35 samples in the study, and those compile just fine while only having 24 GBs of memory and 8 CPUs per task. If anyone has any suggestions or potential fixes, I'd love to hear your response.
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Related Issues (20)
- Remove parameter --gsea_run HOT 1
- URGENT: pin nf-validation version HOT 2
- Dev version: On parameters website list parameter gene_sets_files in section GSEA HOT 1
- Name of blocking variable not correctly recognized HOT 7
- Continuous covariates HOT 6
- Please pin the version of the nf-validation plugin! HOT 1
- Error with samplesheet.csv with two column headers that have prefix in common HOT 8
- release differentialabundance HOT 1
- Process `NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE (gencode)` terminated with an error exit status (125) HOT 4
- Error in TABULAR_TO_GSEA_CHIP HOT 1
- GSEA html reports have broken links to png and TSV files HOT 1
- Failed to publish file => double forward slashes
- Auto-format sample names HOT 2
- PosixFileAttributeView
- Missing colour and hover labels in interactive report volcano plot HOT 4
- Normalized/Raw data mishap on the report HOT 1
- Requests: Enhancements to DESeq2 csv outputs and PDF outputs
- For spike-in analysis, remove control features from outputs
- How to use `--transcript_length_matrix` with nf-core/rnaseq `--aligner star_rsem` output? HOT 2
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