I think the key part in your output is this:
********* Warning: One or more sequences appear to contain invalid amino acid codes. ********* I think this is a warning that we put in to warn that X!Tandem may crash because of your database. You should check your database for validity. Perhaps there are some strange characters in one of the sequences that causes X!Tandem to crash sometimes, but not Comet. We have seen this before. Eric *From:* [email protected] [mailto: [email protected]] *On Behalf Of *zeyu sun *Sent:* Monday, October 06, 2014 7:45 AM *To:* [email protected] *Subject:* Re: [spctools-discuss] X!tandem error thank you Jimmy. I will try the search w/o refinement. I will let you know if the problem solved. SunSun On Monday, October 6, 2014 1:13:01 AM UTC+8, Jimmy Eng wrote: I don't know what the issue is with X!Tandem but just wanted to comment on an unrelated issue which is that you should think twice about using X!Tandem's refinement mode, especially if you are going to push those search results through PeptideProphet or even simple target-decoy FDR. All proteins that make it to the refinement step (and their corresponding peptides identified before or after refinement) will all have distorted/high statistics. Here are two publications that discuss this problem: http://www.ncbi.nlm.nih.gov/pubmed/19947654 http://www.ncbi.nlm.nih.gov/pubmed/21288048 The simple solution is to not use refinement mode. On Sun, Oct 5, 2014 at 1:09 AM, zeyu sun <[email protected] <javascript:>> wrote: Hi, Dear SPC users and developers: I'm wondering if anyone have some clue or remedy to the problem I have with the X!tandem search in TPP(v4.7.1): I have some Orbitrap Velos data in RAW and converted them to mzXML files by MSconverter (ProteoWizard). I ran the Comet pipeline on them and everything was just fine. However, when I search the same mzXMLs by Tandem, some of those files gave error reports: _________________________________________ X! TANDEM Jackhammer TPP (2013.06.15.1 - LabKey, Insilicos, ISB) Loading spectra (mzParser)............................ loaded. Spectra matching criteria = 55267 Pluggable scoring enabled. Starting threads . started. Computing models: 12345678 ********* Warning: One or more sequences appear to contain invalid amino acid codes. ********* 9 sequences modelled = 9 ks Model refinement: partial cleavage .......... done. finishing refinement ... done. Creating report: initial calculations ..... done. sorting ..... done. finding repeats ..... done. evaluating results ..... done. calculating expectations ..... done. writing results ..... done. command "c:\Inetpub\tpp-bin\tandem c:/Inetpub/wwwroot/ISB/data/xxx.tandem.params" failed: Unknown error Command FAILED RETURN CODE:65280 _________________________________________ Despite this error message, the .tandem files were generated, When I use the command tandem2XML to convert the .tandem files to .pep.xml, as expected, it didn't work out: Operation not permitted Command FAILED RETURN CODE:256 It only happens in few mzXML files, not all of them. And Comet runs OK on all files, so I guess the mzXMLs should be fine. I further checked .tandem files, looks like they contain all necessary parts of Xtandem search results, and all spectra-peptide matches were listed there with scores. I just don't know why such files still gave error message and cannot go through tandem2XML. Please help! Thank you very much! SunSun -- 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 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.
