error in DIA:SILICOLIBRARYGENERATION

[reem-abouward]

Description of the bug

I am trying to analyse a few DIA samples and ran into the following errors:

`NFCORE_QUANTMS:QUANTMS:DIA:SILICOLIBRARYGENERATION (UP000005640_9606.fasta)` terminated with an error exit status (140) --
`NFCORE_QUANTMS:QUANTMS:DIA:DIANN_PRELIMINARY_ANALYSIS (20240805_DRIX089_10pct_20)` terminated with an error exit status (137)

I managed to get to the next steps by allowing 10 retries in the config.

process {
    errorStrategy = 'retry'
    maxRetries = 10
    memory = { 200.GB * task.attempt }
}

Not sure if this is an expected problem or if how I "fixed" it is normal.

I then ran into another issue which was previously reported #427

I attached the log, sdrf and config files.

Relevant files

Archive.zip

System information

Nextflow version 24.10.2
Hardware: HPC
Executor: slurm
Container: Singularity
version 1.3.0
bigbio/quantms r 1.3.0.

[jpfeuffer]

Hi!

Yes, this sounds like a memory or time limit that is reached by the SLURM job.
The way you solved it sounds reasonable but maybe you can lower the value a little and/or play with the step's time limit as well.
How big is your fasta and how many variable modifications are you using?

[ypriverol]

@reem-abouward This is my slurm codon config, https://github.com/bigbio/quantms/blob/dev/conf/pride_codon_slurm.config you can take some ideas from there about how to configure DIANN_PRELIMINARY_ANALYSIS

[reem-abouward]

Hi!

Yes, this sounds like a memory or time limit that is reached by the SLURM job. The way you solved it sounds reasonable but maybe you can lower the value a little and/or play with the step's time limit as well. How big is your fasta and how many variable modifications are you using?

Thanks for you reply.
fasta is 13.7 MB. I have 3 variable modifications.