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]>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]> 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%[email protected]><spctools-discuss%2Bunsubscrib > [email protected]> > > > >> <spctools-discuss%[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%[email protected]><spctools-discuss%2Bunsubscrib > [email protected]> > > > >> <spctools-discuss%[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%[email protected]><spctools-discuss%2Bunsubscrib > [email protected]> > > > >> <spctools-discuss%[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%[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. > 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. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
