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Re: [wgs-assembler-users] Long time for PacBiocorrection
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From: Francois S. <fra...@ir...> - 2013-10-04 06:45:03
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Dear all I have followed the instructions (re-install from SVN from fresh download for CA, kmer and even samtools), and just ran the runCorrection.sh... But it failed again.. Have an idea ? Do I have to re-run everything from scratch ? here is the command qsub -A Glabcorr -cwd -V -S /bin/sh -q highmem.q -e $HOME/jobs/ -o $HOME/jobs -v LD_LIBRARY_PATH=$HOME/lib:$LD_LIBRARY_PATH,PATH=$HOME/scripts:$HOME/bin:/home/sabotf/bin:/usr/local/amos-3.1.0/bin:$PATH -pe ompi 12 -l mem_free=128g -cwd -N "pBcR_correct_asm_Glabcorr" -j y -o /dev/null /data/projects/assembling-glab//tempTog5681_corrected/runCorrection.sh I joined the runCorrection.sh script as well as the asm.layout.err files here On 30/09/2013 23:33, Serge Koren wrote: > From your output, it looks like the script is stuck trying to run the correction step. There should be only one correction step. However, your step is failing and as a result, the script sees that correction did not run and tries to run it again, in an infinite loop. This bug should be fixed in the latest source code in the repository. > > As far as why the actual correction step is failing, it looks like the CA version that is included with smrtportal is not CA7.0 but a development version which had some bugs calculating which partition a sequence belongs to. Again, this should be fixed in the latest source code in the repository. As a workaround, you can try lowering the number of partitions (the -p parameter in runCorrection.sh). I would recommend setting it to #threads +1. You can then run the runCorrection.sh script by hand and once there is an asm.layout.success file, re-launch the full correction which will then pick up after this step. > > Sergey > > On Sep 30, 2013, at 4:46 AM, Francois Sabot <fra...@ir...> wrote: > >> Hi >> >> Still have a weird bug, it cannot find (again) bank-transact, even if >> AMOS is in the path (I checked) >> >> Here is the end of my asm.layout error for this step >> >> Using partition 10 to re-estimate insert sizes, total partitions so far >> 1/200 >> Using partition 58 to re-estimate insert sizes, total partitions so far >> 2/200 >> Using partition 66 to re-estimate insert sizes, total partitions so far >> 3/200 >> Using partition 83 to re-estimate insert sizes, total partitions so far >> 4/200 >> Using partition 118 to re-estimate insert sizes, total partitions so far >> 5/200 >> Using partition 122 to re-estimate insert sizes, total partitions so far >> 6/200 >> Using partition 136 to re-estimate insert sizes, total partitions so far >> 7/200 >> Using partition 163 to re-estimate insert sizes, total partitions so far >> 8/200 >> Using partition 175 to re-estimate insert sizes, total partitions so far >> 9/200 >> Using partition 200 to re-estimate insert sizes, total partitions so far >> 10/200 >> openLayFile()-- Failed to open 'asm.200.olaps' for reading: No such file >> or directory >> Couldn't open 'asm.200.olaps' for read: No such file or directory from 0-0 >> >> IlluminaTog5681 >> 400.00 +- 100.00 -> 315.38 +- 76.35 I 37774891/37919939 >> samples external happy 34167579 sad 112016534 >> N/A +- N/A -> 845.33 +- 1030.84 O 198321/218601 samples >> N/A +- N/A -> 2521.31 +- 1937.73 N 65640/69560 samples >> N/A +- N/A -> 2592.02 +- 2017.69 A 55226/58297 samples >> >> Tog5681_corrected >> Filtering mates >> openLayFile()-- Failed to open 'asm.200.olaps' for reading: No such file >> or directory >> Couldn't open 'asm.200.olaps' for write: No such file or directory from 0-0 >> CorrectPacBio.cc:445: int main(int, char**): Assertion `system(command) >> == 0' failed. >> >> Failed with 'Aborted' >> >> Backtrace (mangled): >> >> /home/sabotf/sources/wgs/Linux-amd64/bin//(_Z17AS_UTL_catchCrashiP7siginfoPv+0x27)[0x412797] >> /lib64/libpthread.so.0[0x3bdd20f500] >> /lib64/libc.so.6(gsignal+0x35)[0x3bdce328a5] >> /lib64/libc.so.6(abort+0x175)[0x3bdce34085] >> /lib64/libc.so.6[0x3bdce2ba1e] >> /lib64/libc.so.6(__assert_perror_fail+0x0)[0x3bdce2bae0] >> /home/sabotf/sources/wgs/Linux-amd64/bin//(main+0x2cf2)[0x40e742] >> /lib64/libc.so.6(__libc_start_main+0xfd)[0x3bdce1ecdd] >> /home/sabotf/sources/wgs/Linux-amd64/bin//[0x40b989] >> >> Backtrace (demangled): >> >> [0] /home/sabotf/sources/wgs/Linux-amd64/bin//::AS_UTL_catchCrash(int, >> siginfo*, void*) + 0x27 [0x412797] >> [1] /lib64/libpthread.so.0() [0x3bdd20f500] >> [2] /lib64/libc.so.6::(null) + 0x35 [0x3bdce328a5] >> [3] /lib64/libc.so.6::(null) + 0x175 [0x3bdce34085] >> [4] /lib64/libc.so.6() [0x3bdce2ba1e] >> [5] /lib64/libc.so.6::(null) + 0 [0x3bdce2bae0] >> [6] /home/sabotf/sources/wgs/Linux-amd64/bin//::(null) + 0x2cf2 [0x40e742] >> [7] /lib64/libc.so.6::(null) + 0xfd [0x3bdce1ecdd] >> [8] /home/sabotf/sources/wgs/Linux-amd64/bin//() [0x40b989] >> >> GDB: >> >> >> Any idea ?? >> >> Francois >> >> On 27/09/2013 13:12, Francois Sabot wrote: >>> The script still continues to generate correction steps... >>> >>> Here are the asm.layout.err for run 25 and the output of run24 >>> >>> Francois >>> >>> PS: I changed the -t value >>> >>> On 25/09/2013 18:17, Serge Koren wrote: >>>> Hi, >>>> >>>> There is only one step in runCorrection.sh. If you are using CA 7.0, >>>> there is a known bug in the code that causes it to fail. The wiki >>>> documents a workaround: >>>> http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=PacBioToCA#Error_in_runCorrection.sh_Step >>>> >>>> Re-launching the script will restart the step from the beginning. The >>>> output of the step is in asm.layout.err. If you can share this, it might >>>> give more information on how far the step is and why it may be failing. >>>> >>>> Sergey >>>> >>>> On Sep 23, 2013, at 5:22 AM, Francois Sabot <fra...@ir... >>>> <mailto:fra...@ir...>> wrote: >>>> >>>>> Hi folks >>>>> >>>>> I am running the PacBioToCa on my entire set of data (coverage 12x >>>>> PacBio, 55x Illumina, genome size ~ 400-450 Mb). >>>>> >>>>> I have few weird errors of missed linked, and i re-launch regularly the >>>>> script to ensure its completion. >>>>> >>>>> My question s how can you calculate the numbers of steps in the >>>>> runCorrection.sh part ? It is already on the 19th one, and it ran for >>>>> days.... >>>>> >>>>> Can someone help me ? >>>>> >>>>> Francois >>>>> >>>>> -- >>>>> -------------------------------------------------------- >>>>> Francois Sabot, PhD >>>>> >>>>> Be realistic. Demand the Impossible. >>>>> http://bioinfo.mpl.ird.fr/ >>>>> http://www.mpl.ird.fr/rice >>>>> ----------------------------------------- >>>>> UMR DIversity, Adaptation & DEvelopment >>>>> Centre IRD >>>>> 911, Av Agropolis BP 64501 >>>>> 34394 Montpellier Cedex 5 >>>>> France >>>>> Phone: +33 4 67 41 64 18 >>>>> ----------------------------------------- >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! >>>>> 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, >>>>> SharePoint >>>>> 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack >>>>> includes >>>>> Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. >>>>> http://pubads.g.doubleclick.net/gampad/clk?id=58041151&iu=/4140/ostg.clktrk_______________________________________________ >>>>> wgs-assembler-users mailing list >>>>> wgs...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/wgs-assembler-users >>>> >>> >> >> -- >> -------------------------------------------------------- >> Francois Sabot, PhD >> >> Be realistic. Demand the Impossible. >> http://bioinfo.mpl.ird.fr/ >> http://www.mpl.ird.fr/rice >> ----------------------------------------- >> UMR DIversity, Adaptation & DEvelopment >> Centre IRD >> 911, Av Agropolis BP 64501 >> 34394 Montpellier Cedex 5 >> France >> Phone: +33 4 67 41 64 18 >> ----------------------------------------- >> > > > -- -------------------------------------------------------- Francois Sabot, PhD Be realistic. Demand the Impossible. http://bioinfo.mpl.ird.fr/ http://www.mpl.ird.fr/rice ----------------------------------------- UMR DIversity, Adaptation & DEvelopment Centre IRD 911, Av Agropolis BP 64501 34394 Montpellier Cedex 5 France Phone: +33 4 67 41 64 18 ----------------------------------------- |
