error executing process > 'pipeline:process_bams:extract_barcodes (74) '
reedmakGCB opened this issue · 7 comments
Operating System
macOS
Other Linux
No response
Workflow Version
Workflow Execution
Command line
EPI2ME Version
v3.0
CLI command run
nextflow run epi2me-labs/wf-single-cell --fastq /reedm/singleCell/fastq --kit_name 3prime --kit_version v3 --expected_cells 20000 --ref_genome_dir /10x/refdata-gex-GRCh38-2020-A --plot_umaps --merge_bam --max_threads 8 --resources_mm2_max_threads 32 -profile singularity -c nextflow_env.config
Workflow Execution - CLI Execution Profile
singularity
What happened?
Relevant log output
shown in screenshots aboveApplication activity log entry
No response
Were you able to successfully run the latest version of the workflow with the demo data?
yes
Other demo data information
Hi @reedmakGCB I'm sorry you are having issues with the workflow. Could you post the files .nextflow.log please?
Hello!
I tried adding
profiles {
singularity {
singularity {
enabled = true
autoMounts = true
runOptions = '--writable-tmpfs'
}
}
}
and resuming the process from where this error left off however I was then meet with a different error after the pipeline ran some more.
my log file is too big but here is the last few pages of it:
nextflowLog (dragged).pdf
If you can add the log as a text file and not a pdf it will be much smaller and you shoul dbe able to include it all
I went in a added more time and memory for this step to run but it still gives me this error
Hi @reedmakGCB
Sorry for the delay. From your log it appears the you have these resources available.
CPUs: 2 - Mem: 10 GB
OI would recommend giving the workflow at least 30Gb and raising the number of CPUs substantially.
Hi @reedmakGCB,
Version 2.0.0 released today has reworked a lot of the workflows resource requirements. Please give it a try.