Lockfile command not found
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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

Thanks

Oslo Lockfile conda concurrency • 2.2k views
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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.

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How is this related to bioinformatics?

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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

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Ok, please add these details to your Q above, so that the context is clear.

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if you have used conda environment, activate the environment and tool will be available. You can also add bin in conda installation directory to the path and see if it works.

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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.

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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

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I commented out the lockfile step and ran the step. It ran without any error

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