Segmentation error with CometAdapter

[marissaDubbelaar]

Description of the bug

After running the command with the standard test, I retrieve a crashed hard (segfault-like) error coming from CometAdapter. However, I need to mention that it is running through when I use CometAdapter of openms-thirdparty in the terminal.

Command used and terminal output

nextflow run nf-core/mhcquant -profile test,docker --outdir .

Relevant files

[.nextflow.log](https://github.com/user-attachments/fi
.command.log

System information

Nextflow version: 24.10.3.5933
Hardware: Desktop (WSL2)
Executor: local
Container engine: Docker
OS: Linux 5.15.167.4-microsoft-standard-WSL2
Version of nf-core/mhcquan: 2.6.0

[jonasscheid]

Did you run CometAdapter within docker Container or did you build OpenMS and then ran the Adapter?

[marissaDubbelaar]

I ran it in an conda environment and a dockerimage, but this seems to work

[jonasscheid]

@timosachsenberg any idea what could be the reason here?

[timosachsenberg]

Did you run this exact command using same files (including param.txt)?
And does it display same comet version etc.?

Standard output: Running: /usr/local/bin/comet.exe -P/tmp/20250110_131539_514ed47b4c6d_277_1/param.txt -N/tmp/20250110_131539_514ed47b4c6d_277_1/result HepG2_rep2_small.mzML
 Warning - invalid parameter found: export_additional_pepxml_scores.  Parameter will be ignored.
 Comet version "2023.01 rev. 0"

Standard error: Process '/usr/local/bin/comet.exe' crashed hard (segfault-like). Please check the log.