Did you run peptideProphet before calling ProteinProphet? On Wed, Mar 10, 2010 at 5:33 AM, hcadrexler <[email protected]>wrote:
> Thanks, Brian, for your efforts! You may be right regrading the > browser time out - sounds like a reasonable explanation. I will try > the command line approach as you suggested. > The tandem.xml file as well as the log file (HannesTPPlog.txt) are now > uploaded under my username (hcadrexler) on the groups page file. > > > On 9 Mrz., 23:46, Natalie Tasman <[email protected]> wrote: > > To distribute your files, you could try posting them on the groups' file > > page, and then reply with a post containing the filename: > http://groups.google.com/group/spctools-discuss/files > > > > On 3/9/10 2:01 PM, Brian Pratt wrote: > > > > > I had a look at the three mzXML files you uploaded to Insilicos - > > > they're quite large (about 1GB each) and it just takes X!Tandem a long > > > time to process them. I suspect that you're only getting two at a > > > time done in the TPP web interface due to browser timeout, but you can > > > work around that by copying the contents of the "Attempting to run the > > > following commands" window to the command line. > > > As to why you end up with no specta in ProteinProphet - most readers > > > of this list don't have read access to the ISB ftp site, so you're > > > better off just attaching files to an email message that everyone can > > > look at. > > > Hope this helps, > > > Brian > > > On Tue, Mar 9, 2010 at 1:52 AM, hcadrexler <[email protected] > > > <mailto:[email protected]>> wrote: > > > > > In the meantime I managed to get all of my 29 files through the > > > Xtandem pipeline (in tranches of two) up to the point where the > pepXML > > > file is generated (interact.pep.xml). I can look at the data with > the > > > PepXML Viewer and the data look OK (trypsin digest, X! TANDEM > > > (K-SCORE) search engine, quantitation: [none], displaying 797307 of > > > 797307 total spectra, page 1 of 15947, 329503 unique peptides, > 274865 > > > unique stripped peptides, 34263 unique proteins, 5260 single hits), > > > however, when I try to run ProteinProphet I get a "no data" error > > > message: > > > > > . . . reading in c:/Inetpub/wwwroot/ISB/data/Ooocyte/ > > > 20091125_AD_Boiani_oocyte_29.tandem.pep.xml. . . > > > . . . read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with > > > min prob 0.05 > > > no data - quittingEND OUTPUT > > > RETURN CODE:256 > > > ###### End Command Execution ###### > > > > > Does anybody know what to make out of this error massage? > > > > > The TPP log file as well as the Xtandem parameter file are uploaded > to > > > ftp://ftp.systemsbiology.net/pub/incoming/ within the > Hannes_Xtandem > > > folder. > > > > > On 2 Mrz., 10:53, hcadrexler <[email protected] > > > <mailto:[email protected]>> wrote: > > > > Files are now uploaded in one zip file (Hannes_oocyte). Please et > me > > > > know if you need additional information. Good luck! > > > > Hannes > > > > > > On 1 Mrz., 16:14, Brian Pratt <[email protected] > > > <mailto:[email protected]>> wrote: > > > > > > > Oh, and send the xtandem inputs (mzxml and fasta), not the raw > > > files. > > > > > > > On Mon, Mar 1, 2010 at 7:14 AM, Brian Pratt > > > <[email protected] <mailto:[email protected] > >>wrote: > > > > > > > > Just put it in the pub directory, not a subdirectry. > > > Consider using > > > > > > something like gzip to make the files smaller, too. > > > > > > > > On Mon, Mar 1, 2010 at 2:40 AM, hcadrexler > > > <[email protected] <mailto:[email protected] > >>wrote: > > > > > > > >> Hi Brian, > > > > > > > >> I just tried to upload a few .raw files and the fasta db > > > into the pub > > > > > >> folder using filezilla, however, filezilla tells me that I > > > that there > > > > > >> is no adequate directory for the upload (see error > message)?? > > > > > > > >> .............. > > > > > >> Command: STOR > > > /pub/Hannes_20100301/20091125_AD_Boiani_oocyte_03.raw > > > > > >> Response: 550 > > > /pub/Hannes_20100301/ipi.MOUSE.v3.64.fasta: No such > > > > > >> file > > > > > >> or directory > > > > > >> Command: PASV > > > > > >> Response: 550 > > > /pub/Hannes_20100301/20091125_AD_Boiani_oocyte_03.raw: > > > > > >> No such file or directory > > > > > >> Error: Critical file transfer error > > > > > >> ............. > > > > > > > >> Kind regards, > > > > > > > >> Hannes > > > > > > > >> On 26 Feb., 19:18, Brian Pratt <[email protected] > > > <mailto:[email protected]>> wrote: > > > > > >> > Strange indeed. If you can send me a minimum data set > > > that shows the > > > > > >> > problem I could take a look (presumably three files and > > > the fasta db). > > > > > >> If > > > > > >> > they're too big to email, you can ftp toftp:// > > > > > >> insilicos.serveftp.net/pub < > http://insilicos.serveftp.net/pub>. > > > > > >> > Brian > > > > > >> > On Fri, Feb 26, 2010 at 7:10 AM, Hannes Drexler > > > > > >> > <[email protected] > > > <mailto:[email protected]>>wrote: > > > > > > > >> > > Hi Brian, > > > > > > > >> > > thought about it too, however, when I delete the first > two > > > > > >> > > successfully handled files from the sequence and start > > > the database > > > > > >> > > search again with the next / third file of the list, > > > the subsequent > > > > > >> > > two files are also successfully sent through the > > > pipeline. I repeated > > > > > >> > > it a few more times now and to me it looks like as if > > > XTandem database > > > > > >> > > searches are currently only possible in tranches of > > > two. Strange, > > > > > >> > > isn�it? > > > > > > > >> > > Hannes > > > > > > > >> > > 2010/2/24 Brian Pratt <[email protected] > > > <mailto:[email protected]>>: > > > > > >> > > > You'll want to narrow it down to identify the problem > > > - for > > > > > >> example, > > > > > >> > > what > > > > > >> > > > happens when you omit that 3rd file? > > > > > > > >> > > > On Wed, Feb 24, 2010 at 2:04 AM, hcadrexler < > > > > > >> [email protected] <mailto:[email protected] > >> > > > > > >> > > > wrote: > > > > > > > >> > > >> Hi there, > > > > > > > >> > > >> I tried to perform an XTandem search following the > > > XTandem 2009 > > > > > >> > > >> tutorial using my own data (29 mzXML files). The > > > Database search is > > > > > >> > > >> performed for the first two files in the sequence > > > without any > > > > > >> problems > > > > > >> > > >> but then stops and does not proceed any further with > > > the third (and > > > > > >> > > >> subsequent) files. I cannot figure out where the > > > mistake was made. > > > > > >> > > >> Does anybody know why this might happen? > > > > > > > >> > > >> Kind regards, > > > > > > > >> > > >> Hannes > > > > > > > >> > > >> -- > > > > > >> > > >> You received this message because you are subscribed > > > to the Google > > > > > >> > > Groups > > > > > >> > > >> "spctools-discuss" group. > > > > > >> > > >> To post to this group, send email to > > > > > >> [email protected] > > > <mailto:[email protected]>. > > > > > >> > > >> To unsubscribe from this group, send email to > > > > > >> > > >> > > > [email protected]<spctools-discuss%[email protected]> > > > > > > <mailto:spctools-discuss%[email protected]<spctools-discuss%[email protected]> > ><spctools-discuss%2Bunsubscrib > > > [email protected] <mailto:[email protected]>> > > > > > >> > > > <spctools-discuss%[email protected]<spctools-discuss%[email protected]> > > > > > > <mailto:spctools-discuss%[email protected]<spctools-discuss%[email protected]> > ><spctools-discuss%252Bunsub > > > [email protected] <mailto:[email protected]>> > > > > > > > >> > > . > > > > > >> > > >> For more options, visit this group at > > > > > >> > > >>http://groups.google.com/group/spctools-discuss?hl=en > . > > > > > > > >> > > > -- > > > > > >> > > > You received this message because you are subscribed > > > to the Google > > > > > >> Groups > > > > > >> > > > "spctools-discuss" group. > > > > > >> > > > To post to this group, send email to > > > > > >> [email protected] > > > <mailto:[email protected]>. > > > > > >> > > > To unsubscribe from this group, send email to > > > > > >> > > > > > > [email protected]<spctools-discuss%[email protected]> > > > > > > <mailto:spctools-discuss%[email protected]<spctools-discuss%[email protected]> > ><spctools-discuss%2Bunsubscrib > > > [email protected] <mailto:[email protected]>> > > > > > >> > > > <spctools-discuss%[email protected]<spctools-discuss%[email protected]> > > > > > > <mailto:spctools-discuss%[email protected]<spctools-discuss%[email protected]> > ><spctools-discuss%252Bunsub > > > [email protected] <mailto:[email protected]>> > > > > > > > >> > > . > > > > > >> > > > For more options, visit this group at > > > > > >> > > >http://groups.google.com/group/spctools-discuss?hl=en. > > > > > > > >> > > -- > > > > > >> > > You received this message because you are subscribed > > > to the Google > > > > > >> Groups > > > > > >> > > "spctools-discuss" group. > > > > > >> > > To post to this group, send email to > > > > > >> [email protected] > > > <mailto:[email protected]>. > > > > > >> > > To unsubscribe from this group, send email to > > > > > >> > > > > > [email protected]<spctools-discuss%[email protected]> > > > > > > <mailto:spctools-discuss%[email protected]<spctools-discuss%[email protected]> > ><spctools-discuss%2Bunsubscrib > > > [email protected] <mailto:[email protected]>> > > > > > >> > > > <spctools-discuss%[email protected]<spctools-discuss%[email protected]> > > > > > > <mailto:spctools-discuss%[email protected]<spctools-discuss%[email protected]> > ><spctools-discuss%252Bunsub > > > [email protected] <mailto:[email protected]>> > > > > > > > >> > > . > > > > > >> > > For more options, visit this group at > > > > > >> > >http://groups.google.com/group/spctools-discuss?hl=en. > > > > > > > >> -- > > > > > >> You received this message because you are subscribed to the > > > Google Groups > > > > > >> "spctools-discuss" group. > > > > > >> To post to this group, send email to > > > [email protected] > > > <mailto:[email protected]>. > > > > > >> To unsubscribe from this group, send email to > > > > > >> > > > [email protected]<spctools-discuss%[email protected]> > > > > > > <mailto:spctools-discuss%[email protected]<spctools-discuss%[email protected]> > ><spctools-discuss%2Bunsubscrib > > > [email protected] <mailto:[email protected]>> > > > > > >> . > > > > > >> For more options, visit this group at > > > > ... > > > > Erfahren Sie mehr » > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]<spctools-discuss%[email protected]> > . > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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