Cannot read file. Error parsing, exit code: 1

[winnieWei123456]

I have an error reported:
time="08:47:54" level=info msg="Executing Filter v5.1.1"
time="08:47:54" level=info msg="Processing peptide identification files"
time="08:47:54" level=info msg="Parsing /data/48/cwei/glyco/download/search/PDC000270_all/interact.pep.xml"
time="08:47:56" level=error msg="Cannot read file. Error parsing the file "
Process 'PhilosopherFilter' finished, exit code: 1
Process returned non-zero exit code, stopping

log_2025-10-26_08-47-56.txt

Could you please help me figure out what is wrong?

[AimeeD90]

Hi, could you share the interact.pep.xml, combined.prot.xml and FASTA file? I'll need them to identify the error.

[junyao829]

Hi all,

I also faced similar problem previously with such error during Philosopher filter:
"Cannot read file. Error parsing the file "

I found out that it was caused by a /tmp out-of-storage problem and the combined.prot.xml stopped writing afterwards. This can be fixed by mounting /tmp to somewhere else such as /scratch/users/myfolder if you're running fragpipe through a container in HPC.
singularity exec --compat -B /scratch/users/jteow/tmp:/tmp fragpipe_latest.sif

Hope this helps.

Cheers,
Jun