I have bad news to report: gzipping the files sometimes fixes problems, and sometimes not. In fact, we just ran some 1216 files through X!Tandem, and 585 failed with this same "null pointer exception", so it looks like one would tryly need to figure out what's going on with the program and it's parsing of the name....Will provide more of an update tonight if I get a chance....
On Saturday, 25 August 2012 13:10:50 UTC-4, Gautam Saxena wrote: > > Gziping the file seems to have solved the problem for those 35 files. But, > 1) I don't know if it always solves the problem; 2) it causes other > problems: specifically, the resultant pep.xml file now references within > itself the xtandem file with the "gz" extension, and so at least one > downstream program, namely LIBRA, now errors out because it's looking for > an mzXML file that is named with a ".gz.mzXML" extension. Here's a sample > error from Libra: > > Failed to open input file >> '/usr/ia_working_dir/DASH/DASH_Server/JHU_NHLBI/Users/ >> gsaxena_i-a-inc.com/Workflow_Outputs/Centroided_-_Cys_TMT_Zero_0824_50ppm/zTvL-120625_1CPr_CysTMT0 >> .gz.mzXML'. > > > And, less importantly, gziping consumes a little CPU, which adds up if we > have 1000 or so MS files for a given project. > > So, it would be very beneficial if this bug were to be resolved. In case > it helps, here's something else I noticed: > > > 1. In once project in which we had 1216 MS files, 1201 of those files > correctly ran though tandem2xml. However, 15 failed with the same error > message as indicated previously. The input file to tandem2xml was in a > different directory that I referenced with a fully qualified path name, as > in: > > cd /usr/my_working_dir > /usr/ia_working_dir/DASH/DASH_Server/IA_Common/programs/linux_programs/tpp/bin/Tandem2XML > > /usr/some_dir/another_dir/zz85-control-8-003-9 > 0Cw6-zz85-control-8-003-9.pep.xml > > I solved the problem by creating symbolic link called > " zz85-control-8-003-9" in the "/usr/my_working_dir" that pointed to > /usr/some_dir/another_dir/zz85-control-8-003-9 and then tandem2xml > magically worked. > > Also, I'm not sure if this is an additional wrinkle, but my X!Tandem files > have NO extension. (I needed to do this to support LIBRA properly in my > scenario.) > > > On Friday, 24 August 2012 12:16:52 UTC-4, Dave Trudgian wrote: >> >> That's the same problem I saw then. I'll try and have a look at this >> properly on the weekend, or failing that on Monday / Tuesday. I started to >> look through it before, but the input handling is so complex an hour wasn't >> enough to understand it. >> >> We come across this issue a lot now, due to the way our >> mass-spectrometrists commonly name files. >> >> DT >> >> -----Original Message----- >> From: [email protected] [mailto:[email protected]] >> On Behalf Of Jimmy Eng >> Sent: Friday, August 24, 2012 11:11 AM >> To: [email protected] >> Subject: Re: [spctools-discuss] Re: tandem2xml gives "invalid pointer" >> error on linux >> >> FWIW, just doing something as simple as changing the name from >> "zz85-control-8-003-9" to "zz85-control-8-003-9y" allows the conversion to >> go through fine. Hopefully someone with time will look at the convoluted >> input handling in Tandem2XML as the logic being used to parse input file >> name and recognize file extensions is horribly broken. >> >> On Fri, Aug 24, 2012 at 7:56 AM, Dave Trudgian < >> [email protected]> wrote: >> > Gautum, >> > >> > Maybe this is related to the problem I observed that seems filename >> > dependent: >> > >> > https://groups.google.com/d/topic/spctools-discuss/lp9qde0b2OU/discuss >> > ion >> > >> > If you rename the files do they process correctly? Is there anything >> > common about the filenames of the 35 that don't work? If you run >> > Tandem2XML against the gzipped file does it work? >> > >> > DT >> > >> > If you try to run the command with the >> > >> > >> > On Friday, August 24, 2012 9:39:21 AM UTC-5, Gautam Saxena wrote: >> >> >> >> I have TPP v4.5 RAPTURE rev 2, Build 201208061232 (linux) on Centos >> >> 6.3 (all up to date, 64 bit) installed and pretty much working. For >> >> one project, though, we ran tandem2xml on 632 X!Tandem files. For 597 >> >> of such files, it converted fine. For 35 though, we got the "invalid >> >> pointer" error as >> >> follows: >> >> >> >>> *** glibc detected *** >> >>> >> /usr/ia_working_dir/DASH/DASH_Server/IA_Common/programs/linux_programs/tpp/bin/Tandem2XML: >> >> >> >>> free(): invalid pointer: 0x00000000016fba40 *** ======= Backtrace: >> >>> ========= /lib64/libc.so.6[0x3e316753c6] >> >>> /usr/lib64/libstdc++.so.6(_ZNSsD1Ev+0x39)[0x3e34a9d4a9] >> >>> >> >>> /usr/ia_working_dir/DASH/DASH_Server/IA_Common/programs/linux_progra >> >>> ms/tpp/bin/Tandem2XML[0x413821] >> >>> >> >>> /usr/ia_working_dir/DASH/DASH_Server/IA_Common/programs/linux_progra >> >>> ms/tpp/bin/Tandem2XML[0x405f4e] >> >>> /lib64/libc.so.6(__libc_start_main+0xfd)[0x3e3161ecdd] >> >>> >> >>> /usr/ia_working_dir/DASH/DASH_Server/IA_Common/programs/linux_progra >> >>> ms/tpp/bin/Tandem2XML[0x405c89] >> >>> ======= Memory map: ======== >> >>> 00400000-00469000 r-xp 00000000 00:18 32638052 >> >>> /usr/ia_working_dir/DASH/DASH_Server/IA_Common/programs/linux_progra >> >>> ms/tpp/bin/Tandem2XML >> >>> 00669000-0066b000 rw-p 00069000 00:18 32638052 >> >>> /usr/ia_working_dir/DASH/DASH_Server/IA_Common/programs/linux_progra >> >>> ms/tpp/bin/Tandem2XML >> >>> 0066b000-0066d000 rw-p 00000000 00:00 0 >> >>> 016f8000-01719000 rw-p 00000000 00:00 0 [heap] >> >>> 3e31200000-3e31220000 r-xp 00000000 fd:00 6809 /lib64/ld-2.12.so >> >>> 3e3141f000-3e31420000 r--p 0001f000 fd:00 6809 /lib64/ld-2.12.so >> >>> 3e31420000-3e31421000 rw-p 00020000 fd:00 6809 /lib64/ld-2.12.so >> >>> 3e31421000-3e31422000 rw-p 00000000 00:00 0 >> >>> 3e31600000-3e31789000 r-xp 00000000 fd:00 6810 /lib64/libc-2.12.so >> >>> 3e31789000-3e31988000 ---p 00189000 fd:00 6810 /lib64/libc-2.12.so >> >>> 3e31988000-3e3198c000 r--p 00188000 fd:00 6810 /lib64/libc-2.12.so >> >>> 3e3198c000-3e3198d000 rw-p 0018c000 fd:00 6810 /lib64/libc-2.12.so >> >>> 3e3198d000-3e31992000 rw-p 00000000 00:00 0 >> >>> 3e31e00000-3e31e17000 r-xp 00000000 fd:00 6811 >> >>> /lib64/libpthread-2.12.so >> >>> 3e31e17000-3e32017000 ---p 00017000 fd:00 6811 >> >>> /lib64/libpthread-2.12.so >> >>> 3e32017000-3e32018000 r--p 00017000 fd:00 6811 >> >>> /lib64/libpthread-2.12.so >> >>> 3e32018000-3e32019000 rw-p 00018000 fd:00 6811 >> >>> /lib64/libpthread-2.12.so >> >>> 3e32019000-3e3201d000 rw-p 00000000 00:00 0 >> >>> 3e32200000-3e32215000 r-xp 00000000 fd:00 48060 >> >>> /lib64/libz.so.1.2.3 >> >>> 3e32215000-3e32414000 ---p 00015000 fd:00 48060 >> >>> /lib64/libz.so.1.2.3 >> >>> 3e32414000-3e32415000 r--p 00014000 fd:00 48060 >> >>> /lib64/libz.so.1.2.3 >> >>> 3e32415000-3e32416000 rw-p 00015000 fd:00 48060 >> >>> /lib64/libz.so.1.2.3 >> >>> 3e32600000-3e32683000 r-xp 00000000 fd:00 4968 /lib64/libm-2.12.so >> >>> 3e32683000-3e32882000 ---p 00083000 fd:00 4968 /lib64/libm-2.12.so >> >>> 3e32882000-3e32883000 r--p 00082000 fd:00 4968 /lib64/libm-2.12.so >> >>> 3e32883000-3e32884000 rw-p 00083000 fd:00 4968 /lib64/libm-2.12.so >> >>> 3e33a00000-3e33a10000 r-xp 00000000 fd:00 6655 >> >>> /lib64/libbz2.so.1.0.4 >> >>> 3e33a10000-3e33c0f000 ---p 00010000 fd:00 6655 >> >>> /lib64/libbz2.so.1.0.4 >> >>> 3e33c0f000-3e33c11000 rw-p 0000f000 fd:00 6655 >> >>> /lib64/libbz2.so.1.0.4 >> >>> 3e34200000-3e34216000 r-xp 00000000 fd:00 6814 >> >>> /lib64/libgcc_s-4.4.6-20120305.so.1 >> >>> 3e34216000-3e34415000 ---p 00016000 fd:00 6814 >> >>> /lib64/libgcc_s-4.4.6-20120305.so.1 >> >>> 3e34415000-3e34416000 rw-p 00015000 fd:00 6814 >> >>> /lib64/libgcc_s-4.4.6-20120305.so.1 >> >>> 3e34a00000-3e34ae8000 r-xp 00000000 fd:00 6815 >> >>> /usr/lib64/libstdc++.so.6.0.13 >> >>> 3e34ae8000-3e34ce8000 ---p 000e8000 fd:00 6815 >> >>> /usr/lib64/libstdc++.so.6.0.13 >> >>> 3e34ce8000-3e34cef000 r--p 000e8000 fd:00 6815 >> >>> /usr/lib64/libstdc++.so.6.0.13 >> >>> 3e34cef000-3e34cf1000 rw-p 000ef000 fd:00 6815 >> >>> /usr/lib64/libstdc++.so.6.0.13 >> >>> 3e34cf1000-3e34d06000 rw-p 00000000 00:00 0 >> >>> 2adaee375000-2adaee376000 rw-p 00000000 00:00 0 >> >>> 2adaee382000-2adaee389000 rw-p 00000000 00:00 0 >> >>> 7fffc87d1000-7fffc87e6000 rw-p 00000000 00:00 0 [stack] >> >>> 7fffc87ff000-7fffc8800000 r-xp 00000000 00:00 0 [vdso] >> >>> ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] >> >> >> >> >> >> >> >> The program was run as follows: >> >> >> >>> >> >>> /usr/ia_working_dir/DASH/DASH_Server/IA_Common/programs/linux_progra >> >>> ms/tpp/bin/Tandem2XML >> >>> zz85-control-8-003-9 0Cw6-zz85-control-8-003-9.pep.xml >> >> >> >> >> >> I have attached a zipped version of the input file, >> zz85-control-8-003-9. >> >> (Note, you'll need to unzip and then rename the file to get rid of >> >> the ".temp" suffix; then, you should be able to run the above command >> >> exactly as >> >> is.) >> >> >> >> Any clues? >> >> >> >> Thanks in advance. >> >> >> >> Regards, >> >> Gautam >> >> >> >> >> > -- >> > You received this message because you are subscribed to the Google >> > Groups "spctools-discuss" group. >> > To view this discussion on the web visit >> > https://groups.google.com/d/msg/spctools-discuss/-/9ASFYEooFCMJ. >> > >> > To post to this group, send email to [email protected]. >> > To unsubscribe from this group, send email to >> > [email protected]. >> > For more options, visit this group at >> > http://groups.google.com/group/spctools-discuss?hl=en. >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To post to this group, send email to [email protected]. >> To unsubscribe from this group, send email to >> [email protected]. >> For more options, visit this group at >> http://groups.google.com/group/spctools-discuss?hl=en. >> >> >> ________________________________ >> >> UT Southwestern Medical Center >> The future of medicine, today. >> > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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