Hello, You did not report the number of reads you provided.
wc -l counts lines in a file. Don't forget to CC the list ! > ________________________________________ > De : Huanle LIU [elzed...@gmail.com] > Date d'envoi : 15 juillet 2011 09:13 > À : Sébastien Boisvert > Objet : Re: RE : RE : RE : RE : [Denovoassembler-users] what does this > warning mean? > > 1. I am using Ray 1.60. > > 2. My computer: > MAC OS 10.6.7, Processor 3.06 GHz, Memory: 4 GB. > > 3.number of reads: > > there are a lot: > > -rwxr-xr-x staff 24G 10 Jul 00:23 s1.fastq > -rwxr-xr-x staff 24G 10 Jul 01:22 s2.fastq > -rwxr-xr-x staff 2.9G 10 Jul 01:30 s_3_2_sequence.fastq.bz2 > -rwxr-xr-x staff 2.9G 10 Jul 01:37 s_2_2_sequence.fastq.bz2 > -rwxr-xr-x staff 2.8G 10 Jul 01:45 s_3_1_sequence.fastq.bz2 > -rwxr-xr-x staff 2.9G 10 Jul 01:51 s_2_1_sequence.fastq.bz2 > -rw-r--r-- staff 16M 14 Jul 19:29 h.fastq > -rw-r--r-- staff 22M 14 Jul 19:31 d.fastq > -rw-r--r-- staff 61M 14 Jul 19:32 cd.fastq > -rw-r--r-- staff 94M 14 Jul 19:34 ch.fastq > > bash-3.2$ wc -l *.fastq > 610520 cd.fastq > 1017548 ch.fastq > 124592 d.fastq > 92408 h.fastq > all others are under calculating. > > > > On 15/07/2011, at 11:03 PM, Sébastien Boisvert wrote: > >> Hello, >> >> (don't forget to CC the list, this is an open source project !) >> >> Additional questions: >> >> >> 1. Which version of Ray are you using ? >> >> My guess: v1.6.0, v1.6.1 was released yesterday >> >> >> 2. From the error message you gave, it seems that the code fails in a >> library on your Apple computer, not in Ray. >> >> My guess: the error stems somewhere in >> http://www.opensource.apple.com/source/Libc/Libc-166/sys.subproj/sigtramp.c >> >> >> 3. What is your compute system (processors, memory, operating system) ? >> >> My guess: Apple computer >> >> >> 4. How many reads (including the read length) ? >> >> My guess: 2*130367766, 101 nt >> >> >> Hypothesis: >> >> You are running Ray on 2*130367766 Illumina sequences on a Apple Mac >> computer with 2 compute cores and a few GB of memory. >> Then, your system runs out of memory which causes issues with signal >> handling (outside of Ray) and it crashes. >> >> Ray's RingAllocator requested memory to the system, but the system failed, >> the system should have tell Ray that there is no more memory. >> >> >> >>> ________________________________________ >>> De : Huanle LIU [elzed...@gmail.com] >>> Date d'envoi : 15 juillet 2011 08:42 >>> À : Sébastien Boisvert >>> Objet : Re: RE : RE : RE : [Denovoassembler-users] what does this warning >>> mean? >>> >>> Thanks for your quick response. >>> >>> >>> Here is a more complete version of the warning information: >>> >>> >>> >>> Rank 1 has 130367766 sequence reads (completed) >>> >>> *** >>> Step: Sequence partitioning >>> Date: Fri Jul 15 17:15:38 2011 >>> Elapsed time: 4 hours, 31 minutes, 22 seconds >>> Since beginning: 4 hours, 31 minutes, 22 seconds >>> *** >>> >>> >>> Rank 0 is computing vertices & edges [1/130367766] >>> Rank 1 is computing vertices & edges [1/130367766] >>> [biol-dortiz02d:04336] *** Process received signal *** >>> [biol-dortiz02d:04336] Signal: Segmentation fault (11) >>> [biol-dortiz02d:04336] Signal code: (0) >>> [biol-dortiz02d:04336] Failing at address: 0x0 >>> [biol-dortiz02d:04335] *** Process received signal *** >>> [biol-dortiz02d:04335] Signal: Segmentation fault (11) >>> [biol-dortiz02d:04335] Signal code: (0) >>> [biol-dortiz02d:04335] Failing at address: 0x0 >>> [biol-dortiz02d:04335] [ 0] 2 libSystem.B.dylib >>> 0x00007fff86c7b66a _sigtramp + 26 >>> [biol-dortiz02d:04336] [ 0] 2 libSystem.B.dylib >>> 0x00007fff86c7b66a _sigtramp + 26 >>> [biol-dortiz02d:04336] [ 1] 3 ??? >>> 0x00007fff5fc43c98 0x0 + 140734800084120 >>> [biol-dortiz02d:04336] [ 2] 4 ray >>> 0x000000010007a458 >>> _ZN17VerticesExtractor7processEPiP12ArrayOfReadsPbiP12StaticVectorS3_iiP13RingAllocatorbS0_ >>> + 744 >>> [biol-dortiz02d:04336] [ 3] 5 ray >>> 0x00000001000202e2 _ZN7Machine36call_RAY_SLAVE_MODE_EXTRACT_VERTICESEv + 130 >>> [biol-dortiz02d:04336] [ 4] 6 ray >>> 0x0000000100020a8d _ZN7Machine3runEv + 477 >>> [biol-dortiz02d:04336] [ 5] 7 ray >>> 0x0000000100025450 _ZN7Machine5startEv + 3936 >>> [biol-dortiz02d:04336] [ 6] 8 ray >>> 0x000000010007bd8d main + 61 >>> [biol-dortiz02d:04336] [ 7] 9 ray >>> 0x0000000100002c28 start + 52 >>> [biol-dortiz02d:04336] *** End of error message *** >>> [biol-dortiz02d:04335] [ 1] 3 ??? >>> 0x0000000000000000 0x0 + 0 >>> [biol-dortiz02d:04335] [ 2] 4 ray >>> 0x000000010007a458 >>> _ZN17VerticesExtractor7processEPiP12ArrayOfReadsPbiP12StaticVectorS3_iiP13RingAllocatorbS0_ >>> + 744 >>> [biol-dortiz02d:04335] [ 3] 5 ray >>> 0x00000001000202e2 _ZN7Machine36call_RAY_SLAVE_MODE_EXTRACT_VERTICESEv + 130 >>> [biol-dortiz02d:04335] [ 4] 6 ray >>> 0x0000000100020a8d _ZN7Machine3runEv + 477 >>> [biol-dortiz02d:04335] [ 5] 7 ray >>> 0x0000000100025450 _ZN7Machine5startEv + 3936 >>> [biol-dortiz02d:04335] [ 6] 8 ray >>> 0x000000010007bd8d main + 61 >>> [biol-dortiz02d:04335] [ 7] 9 ray >>> 0x0000000100002c28 start + 52 >>> [biol-dortiz02d:04335] *** End of error message *** >>> mpirun noticed that job rank 0 with PID 4335 on node >>> biol-dortiz02d.sols.uq.edu.au exited on signal 11 (Segmentation fault). >>> 1 additional process aborted (not shown) >>> >>> real 271m49.016s >>> user 0m0.253s >>> sys 0m0.610s >>> >>> >>> >>> >>> >>> On 15/07/2011, at 10:26 PM, Sébastien Boisvert wrote: >>> >>> Where did you got this message exactly ? >>> >>> Sébastien >>> ________________________________________ >>> De : Huanle LIU [elzed...@gmail.com] >>> Date d'envoi : 15 juillet 2011 03:28 >>> À : Sébastien Boisvert >>> Objet : Re: RE : RE : [Denovoassembler-users] what does this warning mean? >>> >>> Hi Sébastien, >>> >>> I got this after running Ray for a while. >>> >>> [biol-dortiz02d:04336] *** Process received signal *** >>> [biol-dortiz02d:04336] Signal: Segmentation fault (11) >>> [biol-dortiz02d:04336] Signal code: (0) >>> [biol-dortiz02d:04336] Failing at address: 0x0 >>> [biol-dortiz02d:04335] *** Process received signal *** >>> [biol-dortiz02d:04335] Signal: Segmentation fault (11) >>> >>> >>> >>> Is this a signal of lack of enough computational resource? >>> >>> Best, >>> >>> Huanle >>> >>> On 15/07/2011, at 2:14 PM, Sébastien Boisvert wrote: >>> >>> OK >>> >>> Sébastien >>> ________________________________________ >>> De : Huanle LIU [elzed...@gmail.com] >>> Date d'envoi : 14 juillet 2011 20:52 >>> À : Sébastien Boisvert >>> Objet : Re: RE : [Denovoassembler-users] what does this warning mean? >>> >>> Thanks a lot. Sébastien. >>> >>> This helps. >>> >>> >>> On 15/07/2011, at 9:25 AM, Sébastien Boisvert wrote: >>> >>> In Ray, fastq files must have the extension .fastq. >>> >>> Input files >>> >>> .fasta >>> .fasta.gz (needs HAVE_LIBZ=y at compilation) >>> .fasta.bz2 (needs HAVE_LIBBZ2=y at compilation) >>> .fastq >>> .fastq.gz (needs HAVE_LIBZ=y at compilation) >>> .fastq.bz2 (needs HAVE_LIBBZ2=y at compilation) >>> .sff (paired reads must be extracted manually) >>> .csfasta (color-space reads) >>> >>> Note: file format is determined with file extension. >>> >>> >>> ln -s h.fq h.fastq >>> ln -s d.fq d.fastq >>> mpirun -np 2 ./Ray -k 30 -s h.fastq -s d.fastq -o dh >>> >>> >>> >>> >>> ________________________________________ >>> De : Huanle LIU [elzed...@gmail.com] >>> Date d'envoi : 14 juillet 2011 06:48 >>> À : >>> denovoassembler-users@lists.sourceforge.net<mailto:denovoassembler-users@lists.sourceforge.net> >>> Objet : [Denovoassembler-users] what does this warning mean? >>> >>> Hi there, >>> >>> I have installed Ray 1.6.0. >>> >>> I was able to run those example data sets. >>> https://exchange.ulaval.ca/owa/?ae=PreFormAction&t=IPM.Note&a=ReplyAll&id=RgAAAAAZZi5ERB%2bFQZ6Qw6Fvp4rOBwDEIX8qv6XUS6jz3NiZ5bDIAEGUP51kAADEIX8qv6XUS6jz3NiZ5bDIAOU0xYhDAAAJ# >>> However, when it came to my own data, i always got this warning message: >>> terminate called after throwing an instance of 'std::out_of_range' what(): >>> basic_string::substr >>> >>> The command line i used is : >>> >>> mpirun -np 2 ./Ray -k 30 -s h.fq -s d.fq -o dh >>> >>> >>> Could anyone help me figure out the rub? >>> >>> Thanks in advance. >>> >>> >>> Cheers, >>> >>> Huanle >>> >>> >> >> Sébastien >> >> >> > > Sébastien ------------------------------------------------------------------------------ AppSumo Presents a FREE Video for the SourceForge Community by Eric Ries, the creator of the Lean Startup Methodology on "Lean Startup Secrets Revealed." 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