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.
