Hey Jimmy, I checked in a fix today.
Cheers, -David On Tue, Apr 15, 2014 at 3:05 PM, Jimmy Eng <[email protected]> wrote: > Will, > > Can you send me a copy of your cidtest.sqt file and I'll look into it when > I get a chance? Compress/zip the 11Mb file and either email it to me or > make it available as a download link. Thanks. > > - Jimmy > > > > On Tue, Apr 15, 2014 at 11:30 AM, Will Fondrie <[email protected]> wrote: > >> >> 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]>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. >> > > -- > 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. 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