pipeline:process_bams:stringtie (23)` terminated with an error exit status (143)
Closed this issue · 4 comments
Operating System
Other Linux (please specify below)
Other Linux
No response
Workflow Version
v1.0.3
Workflow Execution
Command line
EPI2ME Version
No response
CLI command run
nextflow.params.yaml.txt
sRunWorkflow.sh.txt
wf.config.txt
Workflow Execution - CLI Execution Profile
None
What happened?
Hello,
The pipeline was stuck at last stringtie step so I canceled and reran, I am now getting the error pipeline:process_bams:stringtie (23)` terminated with an error exit status (143)
trace.txt
test.wf.32348703.out.txt
nextflow.log.txt
Relevant log output
I have uploaded all relevant log files.Application 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
No response
I'm sorry that you're having issues with the workflow. The issue of stringtie hanging on some chromosomes has been reported by several users and something I'm currently looking into.
The exit 143 status code suggests that the cluster terminated your job exceeded at time of memory limit.
I'd suggest raising the number of cores and memory as these appear to be too low
#SBATCH -n 1 # Number of cores
#SBATCH --mem=4G
Hi Neil,
The resources are set to the recommended 64 cores and 256G in the config file, however it still stalls at 95%. It seems to be stuck at chromosome 1, any other recommendations?
Best regards,
Jason
We've released version 2.0.0 which updates the version on stringtie used. It may alleviate this issue.
I will assume this issue to be resolved. Please open a new issue if problems persist.