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]> 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]> 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]>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]>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]> 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. > > >> > Brian > > >> > On Fri, Feb 26, 2010 at 7:10 AM, Hannes Drexler > > >> > <[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]>: > > >> > > > 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]> > > >> > > > 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]. > > >> > > >> To unsubscribe from this group, send email to > > >> > > >> [email protected]<spctools-discuss%2Bunsubscrib > > >> > > >> [email protected]> > > >> <spctools-discuss%[email protected]<spctools-discuss%252Bunsub > > >> [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]. > > >> > > > To unsubscribe from this group, send email to > > >> > > > [email protected]<spctools-discuss%2Bunsubscrib > > >> > > > [email protected]> > > >> <spctools-discuss%[email protected]<spctools-discuss%252Bunsub > > >> [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]. > > >> > > To unsubscribe from this group, send email to > > >> > > [email protected]<spctools-discuss%2Bunsubscrib > > >> > > [email protected]> > > >> <spctools-discuss%[email protected]<spctools-discuss%252Bunsub > > >> [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]. > > >> To unsubscribe from this group, send email to > > >> [email protected]<spctools-discuss%2Bunsubscrib > > >> [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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