Hello Jonas, I was able to process your data with 4.8.0 and verified the crash under 4.6.2. The specific 4.6.2 bug seems to be in InteractParser, it appears resolved in versions 4.7.0 and higher.
-David On Mon, Aug 17, 2015 at 7:19 AM, <r...@mpipz.mpg.de> wrote: > Hi David, > > Thanks a lot for your fast reply! > > I rechecked my command line, but I don't think that I have a "|" (pipe > character) in it. > I also saw that 4.6.2. is not really up to date anymore, I just tried to > stick to it, because I did all my other analyses with it already. If I > don't get it working now with my new data set I might have to install a > newer version. You're right on this point! > I also suspected the error in the 'output_.tandem.pep.xml' and compared > it with a file that did work before. I can't find any difference in the > structure of this file... > The last lines also look normal: > "<search_score name="ascore" value="0"/> > <search_score name="xscore" value="0"/> > <search_score name="expect" value="0.094"/> > </search_hit> > </search_result> > </spectrum_query> > </msms_run_summary> > </msms_pipeline_analysis>" > > I also checked the .mzXML file, but I can't find any difference in the > structure compared to a .mzXML that is working. The only difference I see > is that the retentionTime is more precise in the file that is working (like > retentionTime="PT6.5879S") while it is simplified in the new .mzXML which > is not working (like > retentionTime="PT6S"). Like this one gets of course several peptides from > one retention Time point. I don't know if the program can work with this or > not. > > Thanks, > > Jonas > > Am Mittwoch, 12. August 2015 18:51:06 UTC+2 schrieb ru...@mpipz.mpg.de: >> >> >> Dear folks, >> >> I am using TPP 4.6.2 and the pipeline always ran perfectly. I switched >> now the MS/MS setup and try to run the pipeline with .mgf files that were >> generated with MaxQuant, because I want to have them comparable to my >> former data instead of just working with MaxQuant. With these new .mgf and >> .mzXML files I encounter problems with runing the InteractParser that I >> never had before: >> >> "pc-t3-025:/Input/TPP-4.6.2/build/LinuxMint-x86_64/bin/xinteract -Od >> -dDECOY -EMPI1 output.tandem.pep.xml >> >> /Input/TPP-4.6.2/build/LinuxMint-x86_64/bin/xinteract (TPP v4.6 OCCUPY >> rev 2, Build 201401101400 (linux)) >> >> running: "/Input/TPP-4.6.2/build/LinuxMint-x86_64/bin/InteractParser >> 'interact.pep.xml' 'output.tandem.pep.xml' -X'MPI1' -L'7'" >> file 1: output.tandem.pep.xml >> SUCCESS: CORRECTED data file /Input/150302_STQ05.mzXML in >> msms_run_summary tag ... >> **** glibc detected **** >> */Input/TPP-4.6.2/build/LinuxMint-x86_64/bin/InteractParser: >> free(): invalid next size (fast): 0x0000000001ff6400 **** >> ======= Backtrace: ========= >> /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7f3d52939b96] >> /Input/TPP-4.6.2/build/LinuxMint-x86_64/bin/InteractParser[0x40e827] >> /Input/TPP-4.6.2/build/LinuxMint-x86_64/bin/InteractParser[0x41623a] >> /Input/TPP-4.6.2/build/LinuxMint-x86_64/bin/InteractParser[0x40ae42] >> /Input/TPP-4.6.2/build/LinuxMint-x86_64/bin/InteractParser[0x40a471] >> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7f3d528dc76d] >> /Input/TPP-4.6.2/build/LinuxMint-x86_64/bin/InteractParser[0x409649] >> ======= Memory map: ======== >> 00400000-0072d000 r-xp 00000000 00:1e 133796865 >> /Input/TPP-4.6.2/build/LinuxMint-x86_64/bin/InteractParser >> 0092c000-0092e000 r--p 0032c000 00:1e 133796865 >> /Input/TPP-4.6.2/build/LinuxMint-x86_64/bin/InteractParser >> 0092e000-00933000 rw-p 0032e000 00:1e 133796865 >> /Input/TPP-4.6.2/build/LinuxMint-x86_64/bin/InteractParser >> 00933000-00938000 rw-p 00000000 00:00 0 >> 01fa6000-0203c000 rw-p 00000000 00:00 0 >> [heap] >> 7f3d527c6000-7f3d528bb000 rw-p 00000000 00:00 0 >> 7f3d528bb000-7f3d52a70000 r-xp 00000000 08:02 18050443 >> /lib/x86_64-linux-gnu/libc-2.15.so >> 7f3d52a70000-7f3d52c6f000 ---p 001b5000 08:02 18050443 >> /lib/x86_64-linux-gnu/libc-2.15.so >> 7f3d52c6f000-7f3d52c73000 r--p 001b4000 08:02 18050443 >> /lib/x86_64-linux-gnu/libc-2.15.so >> 7f3d52c73000-7f3d52c75000 rw-p 001b8000 08:02 18050443 >> /lib/x86_64-linux-gnu/libc-2.15.so >> 7f3d52c75000-7f3d52c7a000 rw-p 00000000 00:00 0 >> 7f3d52c7a000-7f3d52c8f000 r-xp 00000000 08:02 18050366 >> /lib/x86_64-linux-gnu/libgcc_s.so.1 >> 7f3d52c8f000-7f3d52e8e000 ---p 00015000 08:02 18050366 >> /lib/x86_64-linux-gnu/libgcc_s.so.1 >> 7f3d52e8e000-7f3d52e8f000 r--p 00014000 08:02 18050366 >> /lib/x86_64-linux-gnu/libgcc_s.so.1 >> 7f3d52e8f000-7f3d52e90000 rw-p 00015000 08:02 18050366 >> /lib/x86_64-linux-gnu/libgcc_s.so.1 >> 7f3d52e90000-7f3d52f8b000 r-xp 00000000 08:02 18050437 >> /lib/x86_64-linux-gnu/libm-2.15.so >> 7f3d52f8b000-7f3d5318a000 ---p 000fb000 08:02 18050437 >> /lib/x86_64-linux-gnu/libm-2.15.so >> 7f3d5318a000-7f3d5318b000 r--p 000fa000 08:02 18050437 >> /lib/x86_64-linux-gnu/libm-2.15.so >> 7f3d5318b000-7f3d5318c000 rw-p 000fb000 08:02 18050437 >> /lib/x86_64-linux-gnu/libm-2.15.so >> 7f3d5318c000-7f3d53271000 r-xp 00000000 08:02 24083896 >> /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.17 >> 7f3d53271000-7f3d53470000 ---p 000e5000 08:02 24083896 >> /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.17 >> 7f3d53470000-7f3d53478000 r--p 000e4000 08:02 24083896 >> /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.17 >> 7f3d53478000-7f3d5347a000 rw-p 000ec000 08:02 24083896 >> /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.17 >> 7f3d5347a000-7f3d5348f000 rw-p 00000000 00:00 0 >> 7f3d5348f000-7f3d534a7000 r-xp 00000000 08:02 18050411 >> /lib/x86_64-linux-gnu/libpthread-2.15.so >> 7f3d534a7000-7f3d536a6000 ---p 00018000 08:02 18050411 >> /lib/x86_64-linux-gnu/libpthread-2.15.so >> 7f3d536a6000-7f3d536a7000 r--p 00017000 08:02 18050411 >> /lib/x86_64-linux-gnu/libpthread-2.15.so >> 7f3d536a7000-7f3d536a8000 rw-p 00018000 08:02 18050411 >> /lib/x86_64-linux-gnu/libpthread-2.15.so >> 7f3d536a8000-7f3d536ac000 rw-p 00000000 00:00 0 >> 7f3d536ac000-7f3d536c2000 r-xp 00000000 08:02 18050463 >> /lib/x86_64-linux-gnu/libz.so.1.2.7 >> 7f3d536c2000-7f3d538c1000 ---p 00016000 08:02 18050463 >> /lib/x86_64-linux-gnu/libz.so.1.2.7 >> 7f3d538c1000-7f3d538c2000 r--p 00015000 08:02 18050463 >> /lib/x86_64-linux-gnu/libz.so.1.2.7 >> 7f3d538c2000-7f3d538c3000 rw-p 00016000 08:02 18050463 >> /lib/x86_64-linux-gnu/libz.so.1.2.7 >> 7f3d538c3000-7f3d538e5000 r-xp 00000000 08:02 18050430 >> /lib/x86_64-linux-gnu/ld-2.15.so >> 7f3d53968000-7f3d53ac6000 rw-p 00000000 00:00 0 >> 7f3d53ae1000-7f3d53ae5000 rw-p 00000000 00:00 0 >> 7f3d53ae5000-7f3d53ae6000 r--p 00022000 08:02 18050430 >> /lib/x86_64-linux-gnu/ld-2.15.so >> 7f3d53ae6000-7f3d53ae8000 rw-p 00023000 08:02 18050430 >> /lib/x86_64-linux-gnu/ld-2.15.so >> 7fff59d18000-7fff59d39000 rw-p 00000000 00:00 0 >> [stack] >> 7fff59de5000-7fff59de6000 r-xp 00000000 00:00 0 >> [vdso] >> ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 >> [vsyscall] >> Aborted >> >> command "/Input/TPP-4.6.2/build/LinuxMint-x86_64/bin/InteractParser >> 'interact.pep.xml' 'output_.tandem.pep.xml' -X'MPI1' -L'7'" *exited with >> non-zero exit code: 34304* >> QUIT - the job is incomplete" >> >> >> Do you have any suggestions how I can fix this? >> >> Many thanks in advance! >> >> Best, >> >> Jonas >> >> >> -- > 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 spctools-discuss+unsubscr...@googlegroups.com. > To post to this group, send email to spctools-discuss@googlegroups.com. > 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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