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icbi-lab / nextNEOpi

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
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Pipeline complete but missing output file(s) for immunogenicity scoring #45

Closed amoschoomy closed 1 year ago

amoschoomy commented 1 year ago

Hello, I managed to run the pipeline on the sample test data. But unfortunately it is missing one of the output files expected by the process immunogencity scoring

[f4/f6a60c] NOTE: Missing output file(s)sample1_Class_I_immunogenicity.tsvexpected by processimmunogenicity_scoring (sample1)-- Error is ignored

Sep-15 11:12:19.578 [Task submitter] INFO  nextflow.Session - [f4/f6a60c] Submitted process > immunogenicity_scoring (sample1)
Sep-15 11:12:20.528 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 557; name: immunogenicity_scoring (sample1); status: COMPLETED; exit: 0; error: -; workDir: /home/uqachoo1/nextNEOpi-1.4.0/work/f4/f6a60c58002a7237fff929c7d11a25]
Sep-15 11:12:20.528 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process `immunogenicity_scoring (sample1)` is unable to find [UnixPath]: `/home/uqachoo1/nextNEOpi-1.4.0/work/f4/f6a60c58002a7237fff929c7d11a25/sample1_Class_I_immunogenicity.tsv` (pattern: `sample1_Class_I_immunogenicity.tsv`)
Sep-15 11:12:20.533 [Task monitor] INFO  nextflow.processor.TaskProcessor - [f4/f6a60c] NOTE: Missing output file(s) `sample1_Class_I_immunogenicity.tsv` expected by process `immunogenicity_scoring (sample1)` -- Error is ignored
amoschoomy commented 1 year ago

Update: So I rerun the pipeline but without the resume parameters and everything is working fine again. Maybe some tips on how to deal with this kind of issue? Previously when I reran it but while still including the resume parameters it just throws off an error that were totally unrelated to the issue I had.

Much appreciated for the help before I were to run any actual real data on here! Thanks!

riederd commented 1 year ago

Hi, this is not an issue. Unfortunately the immunogenicity_scoring code, which is not developed or maintained by us, is sometimes failing, we are expecting this and so this error is ignored as you can see from:

[f4/f6a60c] NOTE: Missing output file(s) sample1_Class_I_immunogenicity.tsv expected by processimmunogenicity_scoring (sample1) -- Error is ignored
riederd commented 1 year ago

I'm closing this issue now. Please feel free to reopen in case something related pops up.