Failed to run, issues related to pvacseq , etc

icbi-lab / nextNEOpi

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction

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Failed to run, issues related to pvacseq , etc #59

Closed CSree closed 2 months ago

CSree commented 8 months ago

Hi, I ran the pipeline on 3 samples, two of them ended with identical slurm outputs as attached below.

The third generated results only in the Fusions folder, but not the epitopes for Class I and Class II. The end of the slurm output is below

The pic below shows the output files of a successful run by my senior colleague a few months ago, that generated filtered and unfiltered epitopes, along with neoFuse related files, for the sample on the left. However for the third sample I that ran [sample 27], the pic on the right shows only the Fusions folder has the output files. The csv file with tumor mutation burden stats is also not generated.

Is this something to do with the pvacseq tool ?
How to detect if the input fastq.gz files were faulty, since the pipeline has run successfully earlier on many samples earlier..

Thanks so much, Chaitra [junior Bioinformatician, NYU Langone]

mantczakaus commented 8 months ago

Hi, I've been having the same issue. I've reported a bug to pvactools https://github.com/griffithlab/pVACtools/issues/1035 - Magda

riederd commented 8 months ago

The first error you get from Sample26 is an issue with the NetMHCStabPan server which is not under our control, if it is permanent you may use the --use_NetMHCstab False option to disable NetMHCstab.

For your Sample27 I'd need the .nextflow.log log file to get an idea what might be the cause for the missing files (screenshots are not very helpful).

Are there any results in results/analyses/sample1/04_variations ? Can you check with: ls -lR results/analyses/sample1/04_variations

CSree commented 8 months ago

Thank you for your prompt responses. Please find attached the nextflow log file, and the list of variations detected. To see if there are sample issues, I am running the pipeline on a sample on which it ran successfully a few months ago, and I will compare the files generated. Please share any other steps I could take. Thanks Nextflow_log.txt variations.txt

riederd commented 8 months ago

Hi, sorry for the late rply

can you also post the following file /gpfs/scratch/cs5359/Projects/Krogsgaardlab/NeoAg/pipeline/Sample27/work/4a/074d749005cea15578a2ed709eb2da/.command.run

riederd commented 2 months ago

No feedback, assuming it as solved