Hello Luis, Thank you so much for your reply. The results from X!Tandem search seem fine to me. I understand that the quality may be poor, however, I have just changed the pipeline to TANDEM. I have used the same RAW files on Comet and got good results. The PARAMS file is the one by default. I have not changed it. Is TANDEM more sensitive than COMET? I mean that It sees the same data as bad which Comet had no problem in processing.
On Wednesday, 17 January 2018 01:14:46 UTC+5:30, Luis wrote: > Hello, > > Can you verify if you are getting any decent results from your XTandem > search? (i.e. open SAMPLE1.tandem.pep.xml in the PepXMLViewer and > examine.) The warnings that you see are indicative of either poor data > quality, or bad search parameters, so you will want to check those as well. > > Cheers, > --Luis > > > On Mon, Jan 15, 2018 at 7:48 PM, Vipul Batra <[email protected] > <javascript:>> wrote: > >> >> On Saturday, 13 January 2018 19:59:06 UTC+5:30, Vipul Batra wrote: >>> >>> I am getting this error : "*Command FAILED * RETURN CODE:65280" every >>> time I am using X!tandem. I have used the same database and mzml files with >>> comet and the commands were successfully run, however, there seems to be an >>> issue with X! TANDEM. I have even tried with different databases e.g. >>> bovine, human, bubalis but no go . Please guide. >>> >> >> Iterations: .........10.........20...... >> WARNING: Mixture model quality test failed for charge (2+). >> WARNING: Mixture model quality test failed for charge (3+). >> WARNING: Mixture model quality test failed for charge (4+). >> WARNING: Mixture model quality test failed for charge (5+). >> model complete after 27 iterations >> command completed in 2 sec >> >> running: "E:/TPP/bin/ProphetModels.pl -i >> /tmp/a06808/params/interact.pep.xml" Analyzing >> /tmp/a06808/params/interact.pep.xml ... >> Parsing search results "e:/TPP/data/raw/SAMPLE1 (X! Tandem (k-score))"... >> => Found 0 hits. (0 decoys, 0 excluded) >> => Total so far: 0 hits. (0 decoys, 0 excluded) >> command completed in 0 sec >> moving tempfile /tmp/a06808/params/interact.pep.xml to interact.pep.xml >> >> running: "E:/TPP/cgi-bin/PepXMLViewer.cgi -I >> /tmp/a06808/params/interact.pep.xml.a06808" >> command "E:/TPP/cgi-bin/PepXMLViewer.cgi -I >> /tmp/a06808/params/interact.pep.xml.a06808" failed: Unknown error >> >> command "E:/TPP/cgi-bin/PepXMLViewer.cgi -I >> /tmp/a06808/params/interact.pep.xml.a06808" exited with non-zero exit code: >> 255 >> QUIT - the job is incomplete >> >> >> >> -- >> 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] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> Visit this group at https://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 https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
