Hello,
I am attempting to run a MudPit analysis through CPAS using Mascot. However, I keep getting an error report with this message:
command "PeptideProphetParser 'all.pep.xml' EXTRAITRS=20" exited with non-zero exit code: 256
Would you, please, be so kind to suggest how can I resolve this. Thank you very much!
With regards,
Sanja Trajkovic |
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| jeckels responded: |
2012-01-25 16:57 |
Hi Sanja,
Can you attach the full .log file for the job? It may contain more details about the cause of the error.
Thanks,
Josh |
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| sanja.trajkovic responded: |
2012-01-26 08:24 |
Hi Josh,
Here is the file. Thank you very much!
Sanja |
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| jeckels responded: |
2012-01-26 09:26 |
Hi Sanja,
The relevant line in the log seems to be:
ERROR: two instrument manufacturers: Thermo Finnigan and ThermoFinnigan
This is a fraction search. Did all of the fractions' mzXML files undergo the same processing? It may be that they have a mismatch in terms of what they state as their instrument manufacturer. The value should be close to the top of each mzXML file, in a line that looks like this:
<msManufacturer category="msManufacturer" value="ThermoFinnigan"/>
If they're not the same, you might be able to just edit the mzXML files directly to make them consistent. It might be a good idea, though, to reconvert from RAW files to mzXML so that all of your fractions undergo consistent processing.
Thanks,
Josh |
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| sanja.trajkovic responded: |
2012-01-26 12:45 |
Hi Josh,
Thank you very much, your suggestion helped for Mascot. I converted all raw files to mzxml again. Hopefully it will work for sequest and xtandem as well.
Thank you,
Sanja |
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all log.txt