OK, the problem solved! I updated to the latest uniprot fasta and the tandem and tandem2XML work fine now. thankyou all! SunSun
On Tuesday, October 7, 2014 7:48:03 AM UTC+8, Brian Hampton wrote: > > Hi SunSun, > > I ran a search today and got the same error. I was using a bovine > database that I downloaded quite a while ago. So I downloaded the latest > version today, appended the CRAP database to it and then ran it through the > decoy utility to create a concatenated forward and reversed sequence > database. Subsequent searches with the new database completed without > error. > > I can only presume the older database became corrupted somehow. I don't > know of a utility that will validate the integrity of a database. If you > know regex or maybe perl you could write a script to look for characters > that are not part of the amino acid code. For me the expedient solution > was to download a fresh version of the database. > > Brian > > On Oct 6, 2014, at 12:35 PM, zeyu sun <[email protected] <javascript:>> > wrote: > > 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] [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]> 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]. >> 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. 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