Hi Sébastien, the assembly is now running, so it seems to be working, thanks :).
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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