Re: [spctools-discuss] TPP 4.6.2 Regressions

[David Shteynberg]

Hi John,

Thank you for the bug report.  In 4.6.2 we introduced a feature that is supposed to autocorrect issues with bad paths to the data files.  Apparently your input has exposed a bug in this code.  It would be very helpful if you could forward this file to us for debugging.

Thanks,
-David

On May 20, 2013 7:45 AM, "John Chilton" <jmch...@gmail.com> wrote:

I have a dataset that InteractParser works on with 4.6.1.

With 4.6.1:

% /opt/galaxy/tools/transproteomic_pipeline/4.6.1-occupy/bin/InteractParser 'peptide_prophet_output.pep.xml' '/mnt/galaxyData/tmp/job_working_directory/022/22672/dataset_26431.dat.pep.xml' -L'7' -E'trypsin'
 file 1: /mnt/galaxyData/tmp/job_working_directory/022/22672/dataset_26431.dat.pep.xml
 processed altogether 19627 results


 results written to file /mnt/galaxyData/tmp/job_working_directory/022/22672/peptide_prophet_output.pep.shtml



But with 4.6.2 there are a couple of problems. One is that the fact the mzML file doesn't end with .mzML causes issues:



% /opt/galaxy/tools/transproteomic_pipeline/4.6.2-occupy/bin/InteractParser 'peptide_prophet_output.pep.xml' '/mnt/galaxyData/tmp/job_working_directory/022/22672/dataset_26431.dat.pep.xml' -L'7' -E'trypsin'
 file 1: /mnt/galaxyData/tmp/job_working_directory/022/22672/dataset_26431.dat.pep.xml
Failed to open input file '/mnt/galaxyData/files/026/dataset_26429.dat.mzML'.
WARNING: cannot open data file /mnt/galaxyData/files/026/dataset_26429.dat.mzML in msms_run_summary tag ...... trying .mzXML ...
Failed to open input file '/mnt/galaxyData/files/026/dataset_26429.dat.mzXML'.
WARNING: cannot CORRECT data file /mnt/galaxyData/files/026/dataset_26429.dat.mzXML in msms_run_summary tag ...
*** glibc detected *** /opt/galaxy/tools/transproteomic_pipeline/4.6.2-occupy/bin/InteractParser: free(): invalid next size (fast): 0x0000000001037be0 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7fbfbb6cdb96]
/opt/galaxy/tools/transproteomic_pipeline/4.6.2-occupy/bin/InteractParser[0x40e661]
/opt/galaxy/tools/transproteomic_pipeline/4.6.2-occupy/bin/InteractParser[0x415d52]
/opt/galaxy/tools/transproteomic_pipeline/4.6.2-occupy/bin/InteractParser[0x40ace2]
/opt/galaxy/tools/transproteomic_pipeline/4.6.2-occupy/bin/InteractParser[0x40a336]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7fbfbb67076d]
/opt/galaxy/tools/transproteomic_pipeline/4.6.2-occupy/bin/InteractParser[0x409749]
======= Memory map: ========
00400000-00730000 r-xp 00000000 fd:01 1189125                            /opt/galaxy/tools/transproteomic_pipeline/4.6.2-occupy/bin/InteractParser
0092f000-00931000 r--p 0032f000 fd:01 1189125                            /opt/galaxy/tools/transproteomic_pipeline/4.6.2-occupy/bin/InteractParser
00931000-00936000 rw-p 00331000 fd:01 1189125                            /opt/galaxy/tools/transproteomic_pipeline/4.6.2-occupy/bin/InteractParser
00936000-0093b000 rw-p 00000000 00:00 0
00fea000-0104d000 rw-p 00000000 00:00 0                                  [heap]
7fbfb4000000-7fbfb4021000 rw-p 00000000 00:00 0
7fbfb4021000-7fbfb8000000 ---p 00000000 00:00 0
7fbfb8e51000-7fbfb8e52000 ---p 00000000 00:00 0
7fbfb8e52000-7fbfb9652000 rw-p 00000000 00:00 0
7fbfbb55a000-7fbfbb64f000 rw-p 00000000 00:00 0
7fbfbb64f000-7fbfbb804000 r-xp 00000000 fd:01 63                         /lib/x86_64-linux-gnu/libc-2.15.so
7fbfbb804000-7fbfbba03000 ---p 001b5000 fd:01 63                         /lib/x86_64-linux-gnu/libc-2.15.so
7fbfbba03000-7fbfbba07000 r--p 001b4000 fd:01 63                         /lib/x86_64-linux-gnu/libc-2.15.so
7fbfbba07000-7fbfbba09000 rw-p 001b8000 fd:01 63                         /lib/x86_64-linux-gnu/libc-2.15.so
7fbfbba09000-7fbfbba0e000 rw-p 00000000 00:00 0
7fbfbba0e000-7fbfbba23000 r-xp 00000000 fd:01 3753                       /lib/x86_64-linux-gnu/libgcc_s.so.1
7fbfbba23000-7fbfbbc22000 ---p 00015000 fd:01 3753                       /lib/x86_64-linux-gnu/libgcc_s.so.1
7fbfbbc22000-7fbfbbc23000 r--p 00014000 fd:01 3753                       /lib/x86_64-linux-gnu/libgcc_s.so.1
7fbfbbc23000-7fbfbbc24000 rw-p 00015000 fd:01 3753                       /lib/x86_64-linux-gnu/libgcc_s.so.1
7fbfbbc24000-7fbfbbd1f000 r-xp 00000000 fd:01 1293                       /lib/x86_64-linux-gnu/libm-2.15.so
7fbfbbd1f000-7fbfbbf1e000 ---p 000fb000 fd:01 1293                       /lib/x86_64-linux-gnu/libm-2.15.so
7fbfbbf1e000-7fbfbbf1f000 r--p 000fa000 fd:01 1293                       /lib/x86_64-linux-gnu/libm-2.15.so
7fbfbbf1f000-7fbfbbf20000 rw-p 000fb000 fd:01 1293                       /lib/x86_64-linux-gnu/libm-2.15.so
7fbfbbf20000-7fbfbc002000 r-xp 00000000 fd:01 10758                      /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7fbfbc002000-7fbfbc201000 ---p 000e2000 fd:01 10758                      /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7fbfbc201000-7fbfbc209000 r--p 000e1000 fd:01 10758                      /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7fbfbc209000-7fbfbc20b000 rw-p 000e9000 fd:01 10758                      /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7fbfbc20b000-7fbfbc220000 rw-p 00000000 00:00 0
7fbfbc220000-7fbfbc238000 r-xp 00000000 fd:01 108                        /lib/x86_64-linux-gnu/libpthread-2.15.so
7fbfbc238000-7fbfbc437000 ---p 00018000 fd:01 108                        /lib/x86_64-linux-gnu/libpthread-2.15.so
7fbfbc437000-7fbfbc438000 r--p 00017000 fd:01 108                        /lib/x86_64-linux-gnu/libpthread-2.15.so
7fbfbc438000-7fbfbc439000 rw-p 00018000 fd:01 108                        /lib/x86_64-linux-gnu/libpthread-2.15.so
7fbfbc439000-7fbfbc43d000 rw-p 00000000 00:00 0
7fbfbc43d000-7fbfbc453000 r-xp 00000000 fd:01 3757                       /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7fbfbc453000-7fbfbc652000 ---p 00016000 fd:01 3757                       /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7fbfbc652000-7fbfbc653000 r--p 00015000 fd:01 3757                       /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7fbfbc653000-7fbfbc654000 rw-p 00016000 fd:01 3757                       /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7fbfbc654000-7fbfbc676000 r-xp 00000000 fd:01 2823                       /lib/x86_64-linux-gnu/ld-2.15.so
7fbfbc6fe000-7fbfbc85e000 rw-p 00000000 00:00 0
7fbfbc874000-7fbfbc876000 rw-p 00000000 00:00 0
7fbfbc876000-7fbfbc877000 r--p 00022000 fd:01 2823                       /lib/x86_64-linux-gnu/ld-2.15.so
7fbfbc877000-7fbfbc879000 rw-p 00023000 fd:01 2823                       /lib/x86_64-linux-gnu/ld-2.15.so
7fffba567000-7fffba588000 rw-p 00000000 00:00 0                          [stack]
7fffba5b0000-7fffba5b1000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
Aborted (core dumped)




But I am still having problems even if I create a symbolic link ending with mzML. 



% ln -s /mnt/galaxyData/files/026/dataset_26429.dat /mnt/galaxyData/files/026/dataset_26429.dat.mzML
% /opt/galaxy/tools/transproteomic_pipeline/4.6.2-occupy/bin/InteractParser 'peptide_prophet_output.pep.xml' '/mnt/galaxyData/tmp/job_working_directory/022/22672/dataset_26431.dat.pep.xml' -L'7' -E'trypsin'
 file 1: /mnt/galaxyData/tmp/job_working_directory/022/22672/dataset_26431.dat.pep.xml
SUCCESS: CORRECTED data file /mnt/galaxyData/files/026/dataset_26429.dat.mzML in msms_run_summary tag ...
*** glibc detected *** /opt/galaxy/tools/transproteomic_pipeline/4.6.2-occupy/bin/InteractParser: free(): invalid next size (fast): 0x0000000001f7bcd0 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7f5909f78b96]
/opt/galaxy/tools/transproteomic_pipeline/4.6.2-occupy/bin/InteractParser[0x40e661]
/opt/galaxy/tools/transproteomic_pipeline/4.6.2-occupy/bin/InteractParser[0x415d52]
/opt/galaxy/tools/transproteomic_pipeline/4.6.2-occupy/bin/InteractParser[0x40ace2]
/opt/galaxy/tools/transproteomic_pipeline/4.6.2-occupy/bin/InteractParser[0x40a336]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7f5909f1b76d]
/opt/galaxy/tools/transproteomic_pipeline/4.6.2-occupy/bin/InteractParser[0x409749]
======= Memory map: ========
00400000-00730000 r-xp 00000000 fd:01 1189125                            /opt/galaxy/tools/transproteomic_pipeline/4.6.2-occupy/bin/InteractParser
0092f000-00931000 r--p 0032f000 fd:01 1189125                            /opt/galaxy/tools/transproteomic_pipeline/4.6.2-occupy/bin/InteractParser
00931000-00936000 rw-p 00331000 fd:01 1189125                            /opt/galaxy/tools/transproteomic_pipeline/4.6.2-occupy/bin/InteractParser
00936000-0093b000 rw-p 00000000 00:00 0
01f2e000-021a7000 rw-p 00000000 00:00 0                                  [heap]
7f5900000000-7f5900021000 rw-p 00000000 00:00 0
7f5900021000-7f5904000000 ---p 00000000 00:00 0
7f59076fc000-7f59076fd000 ---p 00000000 00:00 0
7f59076fd000-7f5907efd000 rw-p 00000000 00:00 0
7f5909e05000-7f5909efa000 rw-p 00000000 00:00 0
7f5909efa000-7f590a0af000 r-xp 00000000 fd:01 63                         /lib/x86_64-linux-gnu/libc-2.15.so
7f590a0af000-7f590a2ae000 ---p 001b5000 fd:01 63                         /lib/x86_64-linux-gnu/libc-2.15.so
7f590a2ae000-7f590a2b2000 r--p 001b4000 fd:01 63                         /lib/x86_64-linux-gnu/libc-2.15.so
7f590a2b2000-7f590a2b4000 rw-p 001b8000 fd:01 63                         /lib/x86_64-linux-gnu/libc-2.15.so
7f590a2b4000-7f590a2b9000 rw-p 00000000 00:00 0
7f590a2b9000-7f590a2ce000 r-xp 00000000 fd:01 3753                       /lib/x86_64-linux-gnu/libgcc_s.so.1
7f590a2ce000-7f590a4cd000 ---p 00015000 fd:01 3753                       /lib/x86_64-linux-gnu/libgcc_s.so.1
7f590a4cd000-7f590a4ce000 r--p 00014000 fd:01 3753                       /lib/x86_64-linux-gnu/libgcc_s.so.1
7f590a4ce000-7f590a4cf000 rw-p 00015000 fd:01 3753                       /lib/x86_64-linux-gnu/libgcc_s.so.1
7f590a4cf000-7f590a5ca000 r-xp 00000000 fd:01 1293                       /lib/x86_64-linux-gnu/libm-2.15.so
7f590a5ca000-7f590a7c9000 ---p 000fb000 fd:01 1293                       /lib/x86_64-linux-gnu/libm-2.15.so
7f590a7c9000-7f590a7ca000 r--p 000fa000 fd:01 1293                       /lib/x86_64-linux-gnu/libm-2.15.so
7f590a7ca000-7f590a7cb000 rw-p 000fb000 fd:01 1293                       /lib/x86_64-linux-gnu/libm-2.15.so
7f590a7cb000-7f590a8ad000 r-xp 00000000 fd:01 10758                      /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7f590a8ad000-7f590aaac000 ---p 000e2000 fd:01 10758                      /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7f590aaac000-7f590aab4000 r--p 000e1000 fd:01 10758                      /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7f590aab4000-7f590aab6000 rw-p 000e9000 fd:01 10758                      /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7f590aab6000-7f590aacb000 rw-p 00000000 00:00 0
7f590aacb000-7f590aae3000 r-xp 00000000 fd:01 108                        /lib/x86_64-linux-gnu/libpthread-2.15.so
7f590aae3000-7f590ace2000 ---p 00018000 fd:01 108                        /lib/x86_64-linux-gnu/libpthread-2.15.so
7f590ace2000-7f590ace3000 r--p 00017000 fd:01 108                        /lib/x86_64-linux-gnu/libpthread-2.15.so
7f590ace3000-7f590ace4000 rw-p 00018000 fd:01 108                        /lib/x86_64-linux-gnu/libpthread-2.15.so
7f590ace4000-7f590ace8000 rw-p 00000000 00:00 0
7f590ace8000-7f590acfe000 r-xp 00000000 fd:01 3757                       /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7f590acfe000-7f590aefd000 ---p 00016000 fd:01 3757                       /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7f590aefd000-7f590aefe000 r--p 00015000 fd:01 3757                       /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7f590aefe000-7f590aeff000 rw-p 00016000 fd:01 3757                       /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7f590aeff000-7f590af21000 r-xp 00000000 fd:01 2823                       /lib/x86_64-linux-gnu/ld-2.15.so
7f590afa9000-7f590b109000 rw-p 00000000 00:00 0
7f590b11f000-7f590b121000 rw-p 00000000 00:00 0
7f590b121000-7f590b122000 r--p 00022000 fd:01 2823                       /lib/x86_64-linux-gnu/ld-2.15.so
7f590b122000-7f590b124000 rw-p 00023000 fd:01 2823                       /lib/x86_64-linux-gnu/ld-2.15.so
7fff465e5000-7fff46606000 rw-p 00000000 00:00 0                          [stack]
7fff4667c000-7fff4667d000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
Aborted (core dumped)

I am very swamped right now, so I will just revert to using 4.6.1, but I thought I would pass along this bug report. 

Thanks, 

-John

--
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-discu...@googlegroups.com.
To post to this group, send email to spctools...@googlegroups.com.
Visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
For more options, visit https://groups.google.com/groups/opt_out.