I've been playing around with the -r flag but I don't think its converting the entire file. It is possible that I just have a misunderstanding of what the -r flag is doing and what the results should be.
When I use: Sqt2XML -r 10 cidtest.sqt The output is a pep.xml file that is only 24 Kb in size. Then, when I use: Sqt2XML -r 1 cidtest.sqt The output is a pep.xml file that is 1.9 Mb. However both of these seem to small to contain the information of my 11 Mb cidtest.sqt file. Also, I would have thought that the -r 10 command should result in a larger file than the -r 1 command. Thank you, Will On Monday, April 14, 2014 4:44:48 PM UTC-4, David Shteynberg wrote: > > The problem is a small bug in this tool that requires you to set the -r > flag . -r sets the max rank of reported peptides: > > Try: > > Sqt2XML -r 10 cidtest.sqt > > > Thanks! > > -David > > > On Mon, Apr 14, 2014 at 11:50 AM, Will Fondrie <[email protected]<javascript:> > > wrote: > >> Here's a Google Drive link to the cidtest.sqt file that I'm working with. >> >> >> https://drive.google.com/file/d/0B0ATSXjfowrdV2ZDQXlTbEMwdVU/edit?usp=sharing >> >> The file was too big to attach to this message. It was generated as the >> output from a ProLuCID search using a *.ms2 file. This was my first time >> trying to convert the *.sqt files from this tool (and in general). >> >> Thanks for the help and the quick reply! >> >> -Will >> >> >> On Monday, April 14, 2014 2:34:38 PM UTC-4, David Shteynberg wrote: >> >>> I can't tell without looking at the file but my best guess is one of the >>> following: >>> >>> A. The sqt could be malformed or corrupted, has this tool generated sqt >>> that you could convert before or was this your first try? >>> >>> B. It cannot find the data file mzML or mzXML per the message >>> >>> If you share the file I could potentially identify the issue. >>> >>> -David >>> >>> >>> >>> >>> On Mon, Apr 14, 2014 at 11:18 AM, Will Fondrie <[email protected]>wrote: >>> >>>> Hi everyone, >>>> >>>> I am trying to convert *.sqt files from my ProLuCID searches into >>>> *.pep.XML using the Sqt2XML tool. >>>> The command I am running is: >>>> >>>> > Sqt2XML cidtest.sqt >>>> >>>> Where "cidtest.sqt" is my example search result, and my sequest.params >>>> file is in the same directory. However, I get the following output: >>>> >>>> params file here: sequest.params >>>> attempting to read mzXML/mzML: Unknown file type. No file loaded. >>>> Done. File created: cidtest.pep.xml >>>> >>>> When I check the *.pep.xml file that was created, it is not nearly as >>>> large as it should be. Any idea's on what I'm doing wrong? >>>> >>>> Thank you, >>>> Will >>>> >>>> -- >>>> You received this message because you are subscribed to the Google >>>> Groups "spctools-discuss" group. >>>> To unsubscribe from this group and stop receiving emails from it, send >>>> an email to [email protected]. >>>> To post to this group, send email to [email protected]. >>>> >>>> Visit this group at http://groups.google.com/group/spctools-discuss. >>>> For more options, visit https://groups.google.com/d/optout. >>>> >>> >>> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected] <javascript:>. >> To post to this group, send email to >> [email protected]<javascript:> >> . >> Visit this group at http://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. >> > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
