On 28/08/13 04:15 AM, Hornung, Bastian wrote: > Hi Sébastien, > > the assembly is now running, so it seems to be working, thanks :).
Thank you for testing the patch. I merged it in the master branch. https://github.com/sebhtml/ray/commit/20d20c1cef4136281b46e14115631a2326920550 > > Bastian > > ________________________________________ > From: Sébastien Boisvert [sebastien.boisver...@ulaval.ca] > Sent: Tuesday, August 27, 2013 4:37 PM > To: Hornung, Bastian > Cc: denovoassembler-users@lists.sourceforge.net > Subject: Re: [Denovoassembler-users] maximum read length for ray > > (Please use the list) > > Hello, > > I think I found the problem. > > > Can you try with the enclosed patch ? > > > To build Ray v2.2.0 with this patch: > > > wget http://sourceforge.net/projects/denovoassembler/files/Ray-v2.2.0.tar.bz2 > wget > https://raw.github.com/sebhtml/patches/master/ray/Ray-v2.2.0-fix-for-amos-and-long-reads.patch > > tar -xjf Ray-v2.2.0.tar.bz2 > cd Ray-v2.2.0 > patch -p1 < ../Ray-v2.2.0-fix-for-amos-and-long-reads.patch > > make -j 20 > > mkdir -p ~/software/ray/2.2.0-1-long-reads-amos > cp Ray~/software/ray/2.2.0-1-long-reads-amos > > > > > -Sébastien > > On 27/08/13 03:58 AM, Hornung, Bastian wrote: >> Okay, that's then obviously not the problem. >> I've for testing purposes installed a version locally, once with different >> parameters, afterwards with the standard parameters, and loaded the PacBio >> data into it. And it runs. >> If I now try it again on our server (both the local linux machine as well as >> the server are Ubuntu 12.04), no matter if I freshly compile it or use the >> already present installation (also without any different installation >> parameters) I get again a stack overflow warning, see the command line >> output: >> >> >> Rank 0 is fetching file >> /home/bastian/data/RAW/test_illumina_read_1/NG-5257_test_read_1.fastq with >> lazy loading (please wait...) >> Rank 3 is fetching file >> /home/bastian/data/RAW/test1_GTCCGC_L008_R2_001_AC0RCJACXX.filt.fastq with >> lazy loading (please wait...) >> Rank 2 is fetching file >> /home/bastian/data/RAW/test1_GTCCGC_L008_R1_001_AC0RCJACXX.filt.fastq with >> lazy loading (please wait...) >> Rank 1 is fetching file >> /home/bastian/data/RAW/test_illumina_read_2/NG-5257_test_read_2.fastq with >> lazy loading (please wait...) >> Rank 4 is fetching file /home/bastian/data/RAW/PacBio/all_ccs.fastq with >> lazy loading (please wait...) >> Rank 4: File /home/bastian/data/RAW/PacBio/all_ccs.fastq (Number 4) has 3699 >> sequences >> Rank 2: File >> /home/bastian/data/RAW/test1_GTCCGC_L008_R1_001_AC0RCJACXX.filt.fastq >> (Number 2) has 9886736 sequences >> Rank 3: File >> /home/bastian/data/RAW/test1_GTCCGC_L008_R2_001_AC0RCJACXX.filt.fastq >> (Number 3) has 9886736 sequences >> Rank 0: File >> /home/bastian/data/RAW/test_illumina_read_1/NG-5257_test_read_1.fastq >> (Number 0) has 34807392 sequences >> Rank 1: File >> /home/bastian/data/RAW/test_illumina_read_2/NG-5257_test_read_2.fastq >> (Number 1) has 34807392 sequences >> Rank 0 wrote >> /home/bastian/data/RAW/test_illumina_untrimmed_matepair_pacbio_ray_k31/NumberOfSequences.txt >> Rank 0 wrote >> /home/bastian/data/RAW/test_illumina_untrimmed_matepair_pacbio_ray_k31/SequencePartition.txt >> >> *** >> Step: Counting sequences to assemble >> Date: Tue Aug 27 09:42:39 2013 >> Elapsed time: 18 seconds >> Since beginning: 18 seconds >> *** >> >> >> Rank 0 is adding sequences to >> /home/bastian/data/RAW/test_illumina_untrimmed_matepair_pacbio_ray_k31/AMOS.afg >> >> Rank 0 is fetching file >> /home/bastian/data/RAW/test_illumina_read_1/NG-5257_test_read_1.fastq with >> lazy loading (please wait...) >> Rank 0 is fetching file >> /home/bastian/data/RAW/test_illumina_read_1/NG-5257_test_read_1.fastq with >> lazy loading (please wait...) >> adRank 0 is fetching file >> /home/bastian/data/RAW/test_illumina_read_2/NG-5257_test_read_2.fastq with >> lazy loading (please wait...) >> Rank 0 is fetching file >> /home/bastian/data/RAW/test_illumina_read_2/NG-5257_test_read_2.fastq with >> lazy loading (please wait...) >> Rank 0 is fetching file >> /home/bastian/data/RAW/test1_GTCCGC_L008_R1_001_AC0RCJACXX.filt.fastq with >> lazy loading (please wait...) >> Rank 0 is fetching file >> /home/bastian/data/RAW/test1_GTCCGC_L008_R1_001_AC0RCJACXX.filt.fastq with >> lazy loading (please wait...) >> Rank 0 is fetching file >> /home/bastian/data/RAW/test1_GTCCGC_L008_R2_001_AC0RCJACXX.filt.fastq with >> lazy loading (please wait...) >> Rank 0 is fetching file >> /home/bastian/data/RAW/test1_GTCCGC_L008_R2_001_AC0RCJACXX.filt.fastq with >> lazy loading (please wait...) >> Rank 0 is fetching file /home/bastian/data/RAW/PacBio/all_ccs.fastq with >> lazy loading (please wait...) >> Rank 0 is fetching file /home/bastian/data/RAW/PacBio/all_ccs.fastq with >> lazy loading (please wait...) >> *** stack smashing detected ***: Ray terminated >> [ssb3:23288] *** Process received signal *** >> [ssb3:23288] Signal: Segmentation fault (11) >> [ssb3:23288] Signal code: (128) >> [ssb3:23288] Failing at address: (nil) >> >> I have no idea what's going on. >> I doubt that I can run the assembly on my local machine, don't think I have >> enough RAM here. >> There shouldn't be any difference between the 2 machines, that's what >> puzzles me. >> >> Any ideas? >> >> Bastian >> >> >> ________________________________________ >> From: Sébastien Boisvert [sebastien.boisver...@ulaval.ca] >> Sent: Monday, August 26, 2013 3:12 PM >> To: Hornung, Bastian >> Cc: denovoassembler-users@lists.sourceforge.net >> Subject: Re: [Denovoassembler-users] maximum read length for ray >> >> On 26/08/13 04:56 AM, Hornung, Bastian wrote: >>> Hi @all, >>> >>> I'd have a technical question about ray: What is the maximum read length, >>> which can be used? >>> I ask because I get a stack overflow (or rather a message that the process >>> has been aborted before it could happen) when I try to run ray with PacBio >>> data (up to 2kb in that set, IIRC), and wonder what the maximum is what ray >>> can take. >>> >> >> It is 65536 nucleotides. >> >>> Best regards, >>> >>> Bastian >>> >>> >>> ------------------------------------------------------------------------------ >>> Introducing Performance Central, a new site from SourceForge and >>> AppDynamics. 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