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]> 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]. > 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]. 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.
