Jimmy et al: Is there a naming pattern/trick that will always work? For example, if I just suffix the X!Tandem filename with say the characters "yyy" or "xml" or if I prefix it in some similar fashion, will that be a workaround for now?
On Sunday, 2 September 2012 12:56:49 UTC-4, Gautam Saxena wrote: > > 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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