nf-core / nf-core/mhcquant

MS2Rescore config change to prevent crash on 16GB computer

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question
Dominant language
Nextflow
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51
Forks
35
Avg merge
1d 10h
Merged PRs (30d)
7

Description

Hello,

I am running DDA analysis from data generated on the timsTOF Bruker instrument. I am currently using a 16GB ram machine on azure with 100GB storage. I was able to change configurations to run comet with this machine (by restricting CPU threads to 2 and memory to 7GB, while also editing core parameters restricting numerical threads to 2 and spectrum batch size to 200). While the comet ran successfully, it kept crashing at the MS2Rescore step (error message below). I was wondering what parameter to fix to make MS2Rescore step run.
Thanks in advance!

Basic details:
nf-core/mhcquant: 2.x
Nextflow: 25.04.7
Size: Standard E2s v3 (2 vcpus, 16 GiB memory)
Apptainer 1.3.1
OS: Ubuntu 22.04

Nextflow code:
nextflow run ~/mhcquant/main.nf
-profile singularity
-c ~/mhcquant_run/conf/xyz.config
--input sample_sheet.tsv
--fasta HUMAN_2014_concat.fasta
--skip_decoy_generation true
--ms2pip_model timsTOF
--ms2pip_model_dir /home/xyz/ms2pip_models
--outdir results_main

I have attached my error message in the pdf below.

Nextflow error.pdf

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First steps

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  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with main.nf and the supplied xyz.config, then inspect the attached Nextflow error PDF to identify where the MS2Rescore process exceeds available resources. Reproduce the run with the documented command and confirm that the MS2Rescore step completes on the stated 16 GiB machine without a crash.

Written by the indexing model from the issue text.

Assessment

Tech stack
ubuntu
Domain
devops
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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