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Immortalin / peptide-shaker

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String index or t of range #31

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
Dear Colleague,

For the first time I am using peptide shaker and wondered if you can help me 
with the problems that can be found in the files attached.

Many thanks!

> What steps will reproduce the problem?
I've generated MGF files out of the Thermo RAW data (.raw) using Mascot Daemon. 
MGF (.mgf) and Mascot Distiller (.rov) files were generated. The Distiller 
files (.rov) were used to Mascot database search in Mascot Distiller to 
generate mascot search results (.dat). 
Then I loaded in PeptideShaker these .mgf and .dat files plus the fasta file I 
used in Distiller. 

> What is the expected output? What do you see instead?
There was an error to all files loaded as specified in the attached figure.

> What version of the product are you using? On what operating system?
Latest version of distiller, 2.2.2 of Daemon, and PeptideShaker-0.22.5.

> Please provide any additional information below.
Please, check the .log attached.

> If the reported issue resulted in the tool crashing, please
> also upload the file called PeptideShaker.log (found in the
> PeptideShaker-X.Y.Z\resources folder).
It is here attached.

Thanks a lot!

Original issue reported on code.google.com by danm...@gmail.com on 23 Jul 2013 at 2:35

Attachments:

GoogleCodeExporter commented 9 years ago 
Getting Mascot data into PeptideShaker can be a bit tricky. Please upload the 
PeptideShaker log file as well (Help menu > Bug Report) and I'll try to find 
out what the problem is. I'd also recommend taking a look at the Mascot tips 
under Troubleshooting on the PeptideShaker main page.

Original comment by harald.b...@gmail.com on 24 Jul 2013 at 1:27

GoogleCodeExporter commented 9 years ago 
Hello Daniel!

Thanks for the log file. As said in my previous email, Mascot distiller 
sometimes gives strange names to the mgf files. As far as I can see, our parser 
for the mascot .dat file failed at parsing the name of the mgf file. Can you 
send me the dat file (preferably per email) so that I make the software 
compatible with your data?

Sorry for the inconvenience,

Marc

Original comment by mvau...@gmail.com on 24 Jul 2013 at 4:48

GoogleCodeExporter commented 9 years ago

Original comment by mvau...@gmail.com on 12 Dec 2013 at 6:38