Repository may be corrupted

[Ales-ibt]

Hello guys!

Thank you for updating the viral taxonomy in VIRify version 2. I installed the new version using nextflow pull.

$ nextflow info EBI-Metagenomics/emg-viral-pipeline project name: EBI-Metagenomics/emg-viral-pipeline repository : https://github.com/EBI-Metagenomics/emg-viral-pipeline local path : /homes/ales/.nextflow/assets/EBI-Metagenomics/emg-viral-pipeline main script : virify.nf revisions : master (default) bugfix/contig-tax-assign-unkown-taxa dev docker ete3 feature/cwl-mgnify-proteindb-integration no_bitscore_filter no_pprmeta pprmeta_score v0.1 [t] v0.2.0 [t] v0.2.0-no-pprmeta [t] v0.3.0 [t] v0.4.0 [t] v1.0 [t] v1.1 [t] v2.0.0 [t]

And I run the pipeline with:

$ nextflow run EBI-Metagenomics/emg-viral-pipeline -r v2.0.0 --fasta $sample.fasta -profile ebi,singularity

I am now testing the tool and I am having problems running the program in a large number of samples. I have 261 hybrid assemblies of bacterial isolates and every time I launch the jobs in LSF I have around 70% of the samples with the following Nextflow error:

N E X T F L O W ~ version 21.10.0 Unknown error accessing project 'EBI-Metagenomics/emg-viral-pipeline' -- Repository may be corrupted: /homes/ales/.nextflow/assets/EBI-Metagenomics/emg-viral-pipeline

This is an example of the output in the .nextflow.log:

$ cat .nextflow.log Aug-04 12:39:30.572 [main] DEBUG nextflow.cli.Launcher - $> nextflow run EBI-Metagenomics/emg-viral-pipeline -r v2.0.0 --fasta PB_F66.fasta -profile ebi,singularity Aug-04 12:39:30.768 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 21.10.0 Aug-04 12:39:31.655 [main] DEBUG nextflow.scm.AssetManager - Git config: /homes/ales/.nextflow/assets/EBI-Metagenomics/emg-viral-pipeline/.git/config; branch: master; remote: origin; url: https://github.com/EBI-Metagenomics/emg-viral-pipeline.git Aug-04 12:39:31.673 [main] DEBUG nextflow.scm.AssetManager - Git config: /homes/ales/.nextflow/assets/EBI-Metagenomics/emg-viral-pipeline/.git/config; branch: master; remote: origin; url: https://github.com/EBI-Metagenomics/emg-viral-pipeline.git Aug-04 12:39:31.949 [main] DEBUG nextflow.cli.Launcher - Operation aborted org.eclipse.jgit.api.errors.JGitInternalException: Cannot lock /homes/ales/.nextflow/assets/EBI-Metagenomics/emg-viral-pipeline/.git/index. Ensure that no other process has an open file handle on the lock file /homes/ales/.nextflow/assets/EBI-Metagenomics/emg-viral-pipeline/.git/index.lock, then you may delete the lock file and retry. at org.eclipse.jgit.api.CheckoutCommand.call(CheckoutCommand.java:334) at nextflow.scm.AssetManager.checkout(AssetManager.groovy:927) at nextflow.cli.CmdRun.getScriptFile(CmdRun.groovy:382) at nextflow.cli.CmdRun.run(CmdRun.groovy:266) at nextflow.cli.Launcher.run(Launcher.groovy:480) at nextflow.cli.Launcher.main(Launcher.groovy:639) Caused by: org.eclipse.jgit.errors.LockFailedException: Cannot lock /homes/ales/.nextflow/assets/EBI-Metagenomics/emg-viral-pipeline/.git/index. Ensure that no other process has an open file handle on the lock file /homes/ales/.nextflow/assets/EBI-Metagenomics/emg-viral-pipeline/.git/index.lock, then you may delete the lock file and retry. at org.eclipse.jgit.dircache.DirCache.lock(DirCache.java:252) at org.eclipse.jgit.dircache.DirCache.lock(DirCache.java:329) at org.eclipse.jgit.dircache.DirCache.lock(DirCache.java:295) at org.eclipse.jgit.lib.Repository.lockDirCache(Repository.java:1282) at org.eclipse.jgit.api.CheckoutCommand.call(CheckoutCommand.java:268) ... 5 common frames omitted

I am kind of 'solving' the issue by re-launching the jobs but every time I do I have around 70% of the new jobs failing because of this problem with the lock file.

Thanks in advance!

Ales.

[Ales-ibt]

Hello! After removing the repo with nextflow drop EBI-Metagenomics/emg-viral-pipeline and clone the repo in a local directory, the pipeline is running OK.

Bests,

Ales.

[mberacochea]

Cool :)

[hoelzer]

Great!

(just learned about nextflow drop)