Hi David, We will try to compile the PTMProphet code from the svn repository: could you tell me how to access this repository please?
Thanks. Delphine 2015-06-05 21:48 GMT+02:00 David Shteynberg < [email protected]>: > Hi Delphine, > > Unfortunately, with the version of PTMProphet you have this will not be > for you to process this type of data. For linux processing, you will need > to compile and use the latest PTMProphet code from the SVN repository, as > it is not available as a release yet. Alternatively, you can install the > windows version of the code on another machine, migrate your results and > run the binary I sent a link for that includes the latest PTMProphet code. > Our build manager has recently switched jobs so the building of the > software and the releases have been lagging behind the development at the > moment. > > Thanks for you patience, > > -David > > > > On Fri, May 22, 2015 at 5:54 AM, Delphine <[email protected]> wrote: > >> Hello, >> >> I recently asked a question about mods error for the methylation >> identifications with PTMprophet ( >> https://mail.google.com/mail/u/0/#14d15557e5baa348_group_thread_1). You >> helped me to partially solve the problem. Now I have to identify >> methylation, di-methylations and tri-methylations on the same data. I >> modified the interrogation parameter files: >> -comet: >> variable_mod01 = 15.9949 M 0 3 -1 0 >> variable_mod02 = 14.015650 K 0 3 -1 0 >> variable_mod03 = 28.031300 K 0 3 -1 0 >> variable_mod04 = 42.046950 K 0 3 -1 0 >> -xtandem: >> <note type="input" label="residue, modification mass">57.021464@C</note> >> <note type="input" label="residue, potential modification >> mass">15.994915@M,14.015650@K,28.03130@K,42.046950@K</note> >> >> >> I combine the identification results with iprophet (file joined) and >> tried to use PTMprophet on this file. >> >> Here is the command line: >> >> * cd /opt/tpp/data/327_05_01_1704_multimethylations; >> /opt/tpp/bin/PTMProphetParser K,14.0156,K,28.03130,K,42.046950,M,15.9949 >> MZTOL=0.2 >> /opt/tpp/data/327_05_01_1704_multimethylations/327_05_01_014_150417_01_MTCS_0_D_interact.iproph.pep.xml >> 327_05_01_014_150417_01_MTCS_0_D_interact.ptm.pep.xml * >> Here is the error: >> >> >> INFO: Writing file 327_05_01_014_150417_01_MTCS_0_D_interact.ptm.pep.xml ... >> INFO: Reading file >> /opt/tpp/data/327_05_01_1704_multimethylations/327_05_01_014_150417_01_MTCS_0_D_interact.iproph.pep.xml >> ...WARNING: Illegal peptide with unknown mod: DGDPLEK[156]WARNING: Illegal >> peptide with unknown mod: NLM[147]TGMKWARNING: Illegal peptide with unknown >> mod: NLMTGM[147]KWARNING: Illegal peptide with unknown mod: >> K[156]AGESHRWARNING: Illegal peptide with unknown mod: IITNLSK[156]WARNING: >> Illegal peptide with unknown mod: AM[147]NVNPK[156]WARNING: Illegal peptide >> with unknown mod: C[160]PGELPRWARNING: Illegal peptide with unknown mod: >> LTPSM[147]LRWARNING: Illegal peptide with unknown mod: VTAAMGK[156]KWARNING: >> Illegal peptide with unknown mod: VTAAMGKK[156]WARNING: Illegal peptide with >> unknown mod: M[147]ANEVIK[142]WARNING: Illegal peptide with unknown mod: >> M[147]ALTQVRWARNING: Illegal peptide with unknown mod: >> M[147]ADAK[156]QKWARNING: Illegal peptide with unknown mod: >> M[147]ADAKQK[156]WARNING: Illegal peptide with unknown mod: >> AM[147]EAELK[156]WARNING: Illegal peptide with unknown mod: >> K[142]ANSMVKWARNING: Illegal peptide with unknown mod: >> K[142]ANSM[147]VK[156]WARNING: Illegal peptide with unknown mod: >> K[156]ANSM[147]VK[142]WARNING: Illegal peptide with unknown mod: >> KANSMVK[142]WARNING: Illegal peptide with unknown mod: K[142]VPSAPPKWARNING: >> Illegal peptide with unknown mod: KVPSAPPK[142]WARNING: Illegal peptide with >> unknown mod: AEHSELK[156]WARNING: Illegal peptide with unknown mod: >> AEHSELK[156]WARNING: Illegal peptide with unknown mod: VASPK[156]ANKWARNING: >> Illegal peptide with unknown mod: VASPKANK[156]WARNING: Illegal peptide with >> unknown mod: AVDQRNK[142]WARNING: Illegal peptide with unknown mod: >> LATWK[156]PLWARNING: Illegal peptide with unknown mod: AMAEWVK[156]WARNING: >> Illegal peptide with unknown mod: DSFDIIK[156]WARNING: Illegal peptide with >> unknown mod: VPPHM[147]LRWARNING: Illegal peptide with unknown mod: >> LPKAEDRWARNING: Illegal peptide with unknown mod: LKDSLPRWARNING: Illegal >> peptide with unknown mod: KEVPLSRWARNING: Illegal peptide with unknown mod: >> AM[147]LAM[147]FK[156]WARNING: Illegal peptide with unknown mod: >> QAVGPEDK[156]WARNING: Illegal peptide with unknown mod: AM[147]LEVHK[156] >> WARNING: Unrecognized mod on peptide: DILTQLK[170]WARNING: Cannot >> initialize for sequence: DILTQLK[170], unknown mods may exist in spectrum >> 327_05_01_014_150417_01.15465.15465.2WARNING: Illegal peptide with unknown >> mod: SSVC[160]IC[160]K[156] >> Segmentation fault >> >> *Command FAILED* >> >> RETURN CODE:35584 >> >> >> >> Do you have any idea to solve this problem? What I am doing wrong? >> >> Thanks for your help >> >> Delphine >> >> -- >> 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 a topic in the > Google Groups "spctools-discuss" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/spctools-discuss/D3doJvfIepc/unsubscribe > . > To unsubscribe from this group and all its topics, 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.
