DIA_Speclib_Quant cannot pass PhilosopherFilter

[bingnanzhao]

Hi Fragpipe team,

I noticed the DIA_Speclib_Quant workflow cannot successfully pass the PhilosopherFilter step, cancelling remaining 8 tasks. See below the log file:
log_2025-01-02_21-41-31.txt

Many thanks,

Bingnan

[fcyu]

I think it might be due to the file system or IO error. Could you rerun from the FDR validation and filtering by disabling all previous steps?

Thanks,

Fengchao

[bingnanzhao]

Hi Fengchao,

I've tried to start from validation module, and it got stuck at the same step. Here is the log:
[
log_2025-01-03_08-52-35.txt
](url)

And I also tried it both on my local computer and my server.

Many thanks,

Bingnan

[fcyu]

Hi Bingnan,

Is there any temp file but look like pep.xml file in that filer? If yes, Philosopher will read that file and crash.

Best,

Fengchao

[bingnanzhao]

Hi Fengchao,

Yes there are 5 files named as interact-xxxx-.pep.xml. You can see the picture below. And I also find the same type of this temp file in other runs.

I noticed there misses the temp file name in this crashed log file, see it below:

In previous successful runs, there should be the temp file name at the position I pointed out using red. I wonder maybe the issue is due to that?

Many thanks,

Bingnan

[fcyu]

No, your files and command are good. I have no idea why Phiosopher crashed. I will let Yamei @AimeeD90 take a look.

Best,

Fengchao