MLST, VICTORS etc show process failures. How to fix it?

[Michaelijesse]

Kindly guide me how to solve these failures.

Uploaded image for your reference.

Thanking you,

[Michaelijesse]

Process BACANNOT:ARGMINER (29) terminated with an error exit status (127)

Command executed:

run blast with argminer db

run_blasts.py \ blastp \ --query 29.faa \ --db bacannot_dbs_2024_jul_05/argminer_db/diamond.dmnd \ --minid 90 \ --mincov 90 \ --threads 2 \ --out 29_argminer_blastp_onGenes.txt \ --2way > 29_argminer_blastp_onGenes.summary.txt ;

Command exit status: 127

Command output: (empty)

Command error: .command.sh: line 4: run_blasts.py: command not found

[fmalmeida]

Hi @Michaelijesse , Thanks for using the tool.

Can you share the command line you used and the .nextflow.log file so I can try to understand the error?

Thanks. Felipe. :)

[Michaelijesse]

nextflow.241113.log

[Michaelijesse]

nextflow log file attached above

[Michaelijesse]

nextflow run fmalmeida/bacannot --input /home/tbpl/input/samplesheet.yaml --output /home/tbpl/output/2_Assembly --bacannot_db /home/tbpl/omicsdata/zenodo/bacannot_dbs_2024_jul_05 --resfinder_species 'Mycobacterium tuberculosis' --max_cpus 10 -profile docker

[fmalmeida]

Hi @Michaelijesse ,

I do not see anything clearly wrong. But for some reason, Nextflow is not finding these scripts that are located in the bin/ folder.

I will give it a try today to check if it works, but I am afraid there is maybe an env variable or something in the machine clashing with NF ... I hope not.

While I try an execution of the same version later today ... can you try the following to see if the error persists?

1. Run the pipeline identically but using -resume to see if it was random.
2. Run the pipeline with a previous version of Nextflow: 23.10.0.

In case my tests pass, I will have to ask in the Nextflow slack channel, because it will mean it is something with it rather than the pipeline.

Let's work together to get this resolved 💪🏼😁

Best, Felipe.

[fmalmeida]

Just an update,

In my execution of the test profile it worked fine, so I am really curious to see what your retries yield.

If they stay repeating the same, I will have to reach out the Nextflow community in slack to ask for ideas, since it does not seem to be something with the pipeline itself.

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