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Streit-lab / enhancer_annotation_and_motif_analysis

Mini nextflow pipeline for filtering enhancers associated to differentially expressed genes, and then screening for motifs of interest
MIT License
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EXTRACT_GTF_TRANSCRIPTS - change process priority #1

Open dpearton opened 1 week ago

dpearton commented 1 week ago

When I run this on a small bed file I get the following error:

[Task submitter] ERROR nextflow.processor.TaskProcessor - Error executing process > 'EXTRACT_GTF_TRANSCRIPTS'

Caused by: Process requirement exceeds available CPUs -- req: 2; avail: 1 awk -F' ' '$3 ~ /transcript|mRNA/' Gallus_gallus.GRCg6a.97.gtf > Gallus_gallus.GRCg6a.97_transcript_extract.gtf

It seems as if this is set to be "process_low". Could it be upped in priority or constrained to use a single thread?

dpearton commented 1 week ago

Hmmm, I see that process_low does call for 2 cpus. I have no idea why it isn't able to get two cpus when I run it on create. I'll try run it with the create profile (nf-core/configs/create).