Thank you Eric, Is there any tool out there to check the validity of my fasta?
To Jimmy: I just tried the tandem search without refinement, the problem is still there. Thank you all for the reply! SunSun On Monday, October 6, 2014 10:58:12 PM UTC+8, Eric Deutsch wrote: > > 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] <javascript:> [mailto: > [email protected] <javascript:>] *On Behalf Of *zeyu sun > *Sent:* Monday, October 06, 2014 7:45 AM > *To:* [email protected] <javascript:> > *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]> 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]. > 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] <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.
