PhilosopherFilter error: "Cannot read file. Error parsing, exit code: 1"

[dfermin]

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Hello

I'm running Philosopher as part of Fragpipe.

While running my workflow I get an error about a single mzML file:

PhilosopherFilter [Work dir: /home/dfermin/projects/glycoMS/fragPipeWork/out/F20230904_1026]
/usr/local/a2idea/apps/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --mapmods --tag rev_ --pepxml /home/dfermin/projects/glycoMS/fragPipeWork/out/F20230904_1026 --dbbin /home/dfermin/projects/glycoMS/fragPipeWork/out/F20230904_10005 --protxml /home/dfermin/projects/glycoMS/fragPipeWork/out/combined.prot.xml --probin /home/dfermin/projects/glycoMS/fragPipeWork/out/F20230904_10005 --razor
time="20:42:15" level=info msg="Executing Filter  v5.1.0"
time="20:42:15" level=info msg="Fetching protein inference from /home/dfermin/projects/glycoMS/fragPipeWork/out/F20230904_10005"
time="20:42:15" level=info msg="Processing peptide identification files"
time="20:42:15" level=info msg="Parsing /home/dfermin/projects/glycoMS/fragPipeWork/out/F20230904_1026/interact.pep.xml.tmp.qVCMdp"
time="20:42:15" level=info msg="Parsing /home/dfermin/projects/glycoMS/fragPipeWork/out/F20230904_1026/interact.pep.xml"
time="20:42:15" level=error msg="Cannot read file. Error parsing the file "
Process 'PhilosopherFilter' finished, exit code: 1
Process returned non-zero exit code, stopping

~~~~~~~~~~~~~~~~~~~~
Cancelling 465 remaining tasks
## END: Tue Apr  2 20:42:15 EDT 2024

But when I go into that folder I see the file there:

[dfermin in fragPipeWork ]$: ls /home/dfermin/projects/glycoMS/fragPipeWork/out/F20230904_1026
total 19M
-rw-rw-r-- 1 dfermin dfermin  733 Apr  2 20:42 filter.log
-rw------- 1 dfermin dfermin  11M Apr  2 20:38 interact.pep.xml
-rw-rw-r-- 1 dfermin dfermin 1.3M Apr  2 18:00 F20230904_1026_uncalibrated.tsv
-rw-rw-r-- 1 dfermin dfermin 6.5M Apr  2 18:00 F20230904_1026_uncalibrated.pepXML
-rw------- 1 dfermin dfermin    0 Apr  1 22:37 interact.pep.xml.tmp.qVCMdp

I have two questions:

1. Is there any suggestions for who to fix this?
2. Is there a way to run Fragpipe from where it left off rather than starting from the beginning?

Thanks

[danielgeiszler]

You have a temporary interact file that it is also trying to read, probably from a run that was cancelled or crashed. Please delete the temporary interact.pep.xml file and try again.

[dfermin]

Thanks. Will do. Do you know if I execute the fragpipe command again will it pick up where it left off or start the analysis from the beginning?

[danielgeiszler]

You just need to disable the tools that already ran. So if you disable MSFragger and everything in the Validation tab up to FDR Filter and Report, I think it should work.