Entering edit mode
2.8 years ago
priya.bmg
▴
60
Hello
I am trying to setup snakemake workflow to analyse long range sequencing reads in HPC. The script stops when it has lockfiles giving the error: lockfile command not found. I installed lockfile tool in the conda environment. I could find forums suggesting the use of oslo concurrency tool https://github.com/ARMmbed/mbed-ls/issues/130 . I have installed oslo concurrency in the conda enivronment. But, I still get the same error: lockfile command not found. Has anyone across this issue with lockfile tool? Please advice
Script stops running the below lines:
lockfile -r 0 ${LOCKFILE} || exit 1
trap "rm -f ${LOCKFILE}; exit" SIGINT SIGTERM ERR EXIT
Lockfile issues do come up in bioinformatics occasionally - if you could mention your bioinformatics context (as @Santosh suggests) it would get more interest, help more people in the future, and be more appropriate for this forum.
How is this related to bioinformatics?
I am trying to setup snakemake workflow in HPC for analysis of NGS long range sequencing. I have to optimize and customize the scripts for running in HPC. The script stops running, where it has to lockfiles with error:lockfile command not found
Ok, please add these details to your Q above, so that the context is clear.
if you have used conda environment, activate the environment and tool will be available. You can also add
binin conda installation directory to the path and see if it works.I tried activating the environment and I also tried adding the bin folder to the path but it still gives the same error:lockfile command not found.
priya.bmg - did you ever resolve this issue? I'm having the same issue. I'm probably running the same analysis. Any feedback about resolving this issue would be much appreciated
I commented out the lockfile step and ran the step. It ran without any error