nrhorner
commented
5 months ago Hi @KatrinMoller
Thanks for reporting this. You have uncovered a bug, and we'll get a fix out straight away.
Closed KatrinMoller closed 4 months ago
nrhorner
commented
5 months ago Hi @KatrinMoller
Thanks for reporting this. You have uncovered a bug, and we'll get a fix out straight away.
KatrinMoller
commented
5 months ago Any news on this? In the meantime my run stopped since the map_reads function (via minimap2) seems to be storing data for previous samples on the RAM so it filled up. I ran this pipeline (previous version) before with really good results, would love to see an update soon :)
nrhorner
commented
5 months ago Hi @KatrinMoller
There is a fix for this on the prerelease branch. Would you be able to test it out please?
You can use it with nextflow run epi2me-labs/wf-transcriptomes -r prerelease
Thanks,
Neil
KatrinMoller
commented
5 months ago Hi @nrhorner Thanks, I am testing it now, will let you know how it goes.
KatrinMoller
commented
4 months ago @nrhorner So I ran the pipeline using the -r prerelease option and it got very quickly through the commands that previously took ages, so I think that problem was solved. However, now it got stuck in the differential expression analysis: <pipeline:differential_expression:deAnalysis` terminated with an error exit status (1)> There were 3 attempts at solving this but then the pipeline terminated with an error status. The pipeline managed to export .fas, .bam and .bai files for some of the samples, but not all. I think this is an unrelated error to the previous one, perhaps should have another thread for it. Would really appreciate help on solving this, not sure what info you need to figure it out though?
nrhorner
commented
4 months ago Hi @KatrinMoller
Thanks for the update. Yes please open another ticket for the new issue. I'll close this one
Operating System
Windows 10
Other Linux
No response
Workflow Version
v1.0.0
Workflow Execution
Command line
EPI2ME Version
No response
CLI command run
OUTPUT=~/output; ./nextflow run epi2me-labs/wf-transcriptomes \ -profile singularity \ --fastq /hpcdata/Mimir/shared/km100/all_libs \ --de_analysis \ --ref_genome Homo_sapiens.GRCh38.dna_rm.primary_assembly.fa.gz\ --ref_annotation Homo_sapiens.GRCh38.110.gtf.gz \ --ref_transcriptome Homo_sapiens.GRCh38.cdna.all.fa.gz\ --sample_sheet sample_sheet.csv \ --cdna_kit "SQK-PCS111" \ --isoform_table_nrows 10000 \ --out_dir outdir -w workspace_dir \ --threads 64
Workflow Execution - CLI Execution Profile
singularity
What happened?
I am running this pipeline with a rather large dataset (ca 400Gb), so I wanted to utilise all the 64 cores available to me on the server that I am using. One of the last versions of this pipeline has thankfully introduced the option of -threads to determine how many cores should be used. The pipeline was running quite smoothly until it finished
Then it started the and has now, 5 days later, only finished 3 out of the 10 samples. When I checked, this process seems to only be using 1 core.
Is this a bug in the pipeline or are there an additional command I need to use to get minimap2 to run on multiple cores?
Since the process is still running, I am pasting the contents of the "trace" file in here
Relevant log output
Application activity log entry
No response