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marbl / MetaCompass

MetaCompass: Reference-guided Assembly of Metagenomes
https://github.com/marbl/MetaCompass/wiki
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enable --nolock in snakemake workflow, or --unlock on command line #11

Closed taylorreiter closed 5 years ago

taylorreiter commented 5 years ago

Encountered lock error during STAMPS MBL 2019 tutorial. Can you disable locking, or enable --unlock so we can unlock without deleting .snakemake?

@ryanpeek @astrobiomike

MissingInputException in line 42 of /opt/MetaCompass/snakemake/metacompass.iter0.paired.py:
Missing input files for rule merge_reads:
SRR606249_subset10_1.fqSRR606249_subset10_2.fq
unlocking
removed all locks
Error: Directory cannot be locked. Please make sure that no other Snakemake process is trying to create the same files in the following directory:
/output
If you are sure that no other instances of snakemake are running on this directory, the remaining lock was likely caused by a kill signal ora power loss. It can be removed with the --unlock argument.
vcepeda commented 5 years ago

Use the --clobber option.

taylorreiter commented 5 years ago

that did not unlock the snakefile. I had to delete the .snakemake directory.

vcepeda commented 5 years ago

I haven't encountered that problem. --clobber always works for me. If it doesn't work you can delete all the content inside the --output and use the --clobber option. If that doesn't work, please specify the commands you are trying.

taylorreiter commented 5 years ago

This was on a learners machine during a STAMPS MBL 2019 tutorial, I don't have access to the exact command. However, --clobber did not work, and there was no way to unlock the snakefile. Deleting the .snakemake folder worked. Feel free to close the issue as I cannot reproduce the learners compute environment now.