Comments (8)
This seems an issue on NF side, a possible and nicer workaround should be 👍
task.memory ? "--limitBAMsortRAM ${task.memory.toBytes() - 100000000 : ''
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ERROR ~ Error executing process > 'star (UHR_Rep2_ERCC-Mix1_1)'
Caused by:
Not a valid memory value: null
Source block:
prefix = reads[0].toString() - ~/(_R1)?(_trimmed)?(_val_1)?(\.fq)?(\.fastq)?(\.gz)?$/
def avail_mem = task.memory == null ? '' : "--limitBAMsortRAM ${task.memory.toBytes() - 100000000}"
seqCenter = params.seqCenter ? "--outSAMattrRGline ID:$prefix 'CN:$params.seqCenter'" : ''
"""
STAR --genomeDir $index \\
--sjdbGTFfile $gtf \\
--readFilesIn $reads \\
--runThreadN ${task.cpus} \\
--twopassMode Basic \\
--outWigType bedGraph \\
--outSAMtype BAM SortedByCoordinate $avail_mem \\
--readFilesCommand zcat \\
--runDirPerm All_RWX \\
--outFileNamePrefix $prefix $seqCenter \\
"""
@pditommaso, I guess this is being caused by the statement task.memory == null
. Is this something that's changed in the last release? Should this code be replaced with something different?
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Updated and in PR #96 - tests now running. Thanks both!
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Do you think that this will now be a problem?
Line 18 in acd1162
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Hi @edxxgardo,
I've just merged what I hope is a fix into the dev
branch. If you could try running again and see if you still get the same problem, that would be great!
Thanks,
Phil
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Thanks. I'll try and get back to you soon.
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Ok, no more memory error. But, the problem with the never ending process mentioned in #93 is still there.
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Great stuff, thanks! 🎉
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Related Issues (20)
- 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
- Show Salmon-based strand inference in MultiQC report HOT 1
- Add `tximport` for RSEM outputs
- modules missing stub
- Custom content plots missing in MultiQC ouptut HOT 1
- Unable to go from FASTQ to Salmon Quantification
- Add support to use the pipeline with NGS generated using zymo research kit HOT 3
- Stubs all the way down
- NFCORE_RNASEQ takes values from global scope
- Accept uncompressed files, for instance fastq HOT 1
- Test profiles broken for Platform
- Updating picard to 3.2.0 fails pipeline level tests HOT 1
- To use STAR module, how should the GTF file look like
- NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (SRR15731653)` terminated with an error exit status (1)
- Sanity-check the sample names before committing to any data processing
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