peptideprophet error

[zeyu sun]

Dear TPP team:
I came across a error message that I really cannot explain why. Hopefully some of experts here can help me to decode the message. Really appreciated! 
The data was collected from a LTQ-Orbitrap, the search was done by X!tandem within the TPP environment using the default setting "isb_default_input_kscore setting". 

The search result was automatically converted to pep.xml and when I try to filter the results with peptideprophet I got error message like this: 
_____________________________________________________________________________________________________________________________


 run_in c:/Inetpub/wwwroot/ISB/data/data/AIF/20120728/processed; c:\Inetpub\tpp-bin\xinteract  -Nbsa1_3con_filtered.pep.xml -p0.95 -l7 -O bsa1_3con.tandem.pep.xml 

---

c:\Inetpub\tpp-bin\xinteract (TPP v4.5 RAPTURE rev 2, Build 201202031108 (MinGW))

running: "C:/Inetpub/tpp-bin/InteractParser "bsa1_3con_filtered.pep.xml" "bsa1_3con.tandem.pep.xml" -L"7""
 file 1: bsa1_3con.tandem.pep.xml
 processed altogether 4615 results


 results written to file c:/Inetpub/wwwroot/ISB/data/data/AIF/20120728/processed/bsa1_3con_filtered.pep.xml

 direct your browser to http://localhost/ISB/data/data/AIF/20120728/processed/bsa1_3con_filtered.pep.shtml



command completed in 1 sec 

running: "C:/Inetpub/tpp-bin/DatabaseParser "bsa1_3con_filtered.pep.xml""
command completed in 1 sec 

running: "C:/Inetpub/tpp-bin/RefreshParser "bsa1_3con_filtered.pep.xml" "c:/Inetpub/wwwroot/ISB/data/dbase/BOVIN_DECOY.fasta""

---

...skipping 23 lines of output...

---

WARNING: Mixture model quality test failed for charge (3+).
  model complete after 25 iterations
command completed in 1 sec 

running: "C:/Inetpub/tpp-bin/ProphetModels.pl -i bsa1_3con_filtered.pep.xml"
Analyzing bsa1_3con_filtered.pep.xml ...
Parsing search results "c:/Inetpub/wwwroot/ISB/data/data/AIF/20120728/processed/bsa1_3con (X! Tandem (k-score))"...
  => Total of 0 hits.
  => Total of 0 decoy hits.
  => Total of 0 excluded hits.
command completed in 0 sec 

running: "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/Inetpub/wwwroot/ISB/data/data/AIF/20120728/processed/bsa1_3con_filtered.pep.xml"

command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/Inetpub/wwwroot/ISB/data/data/AIF/20120728/processed/bsa1_3con_filtered.pep.xml" failed: Unknown error

command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/Inetpub/wwwroot/ISB/data/data/AIF/20120728/processed/bsa1_3con_filtered.pep.xml" exited with non-zero exit code: 255
QUIT - the job is incomplete

command "c:\Inetpub\tpp-bin\xinteract -Nbsa1_3con_filtered.pep.xml -p0.95 -l7 -O bsa1_3con.tandem.pep.xml" failed: Unknown error

Command FAILED
__________________________________________________________

thank you so much in advance!

sunsun

[Vishal Swaroop]

Is it getting stuck at "PepXMLViewer.cgi"... 

I am not sure if it will help... do you have "tmp" folder under "C:" drive ?

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[zeyu sun]

Thanks for the reply Vishal,
Yes, I do have tmp folder under the C drive.
SunSun

[kshitiz]

Hi,

I am not an expert but I can try to give some clues. Also I work on the linux version.

Your prophet models failed for charge 3+. This is not good and I have never seen this with my data. Do you have a decoy database concatenated and randomised in the database that you used to search with X!Tandem? If yes then are you passing the right parameters in the xinteract command?

The error with PepXMLViewer.cgi is not due to a problem with with the viewer itself but it suggests there was a problem upstream of the viewer and it is complaining because there is no data for it to process. I have seen this one before and it happens when there is no high quality data from the mass spec runs. Try may be changing the default tolerance on your xinteract.

Hope it helps,

Cheers,

Kshitiz Tyagi

[zeyu sun]

Thanks Kshitiz, actually that's what I was guessing. The problem might occur during x!tandem results loading into the xinteract, somehow it did not pick up the tandem results properly. I did used a target-reverse concatenated database and used a quite loose searching parameter, which gives a lot of decoy hits. But just by looking at the pepXML itself, the target hits (BSA only actually) still single out pretty nicely with very low x!tandem expect score. 

SunSun

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