Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • #16
    ok thanks again.
    I will let you know any news and I will upgrade to the 0.6.4b.

    All the best
    Last edited by blu78; 04-11-2010, 12:01 PM.

    Comment


    • #17
      It seems I am having the same problem...
      I am using bfast-0.6.4 and I set the number of threads to 8 I got the "Segmentation fault" error. However when I set it to 4, BFAST works just fine. Was this problem solved?

      Thanks!

      Comment


      • #18
        Originally posted by fennan View Post
        It seems I am having the same problem...
        I am using bfast-0.6.4 and I set the number of threads to 8 I got the "Segmentation fault" error. However when I set it to 4, BFAST works just fine. Was this problem solved?

        Thanks!
        Could you post the results of the "configure" command (during install)?

        Comment


        • #19
          Hi,

          We have the same problem with debian Lenny 64bits: bfast (0.6.4d but also 0.6.2a and 0.6.3c) crashes when running with 8 CPU but not with 4 (our server has 32 cores so we would really want to use as many resources as possible.

          - The configuration phase is the same as blue78 : http://pastebin.com/vW9kXwX9
          - It generates the following config.h : http://pastebin.com/gk57XfP9
          - and for the compilation: http://pastebin.com/jBLjyL2s (it complains a bit about gzread64 not being declared but nothing wrong during the linking)

          We are running the folowwing commands:
          Code:
          WORK_DIR=/data/ngs/solid/PROJETS/Comp_bowtie_bfast/BFAST
          REF_GENOME=/data/ngs/annotations/bfast_indexes/hg19.fa
          BFAST_BIN_DIR=/bioinfo/local/build/bfast_0.6.4d/bin
          NB_THREADS=8
          
          nohup $BFAST_BIN_DIR/bfast match -f $REF_GENOME -n $NB_THREADS -A 1 -r $WORK_DIR/FastQ/reads100000.200.fastq > $WORK_DIR/Bmf/bmfbfast.matches.file.hg19.200.bmf
          The result is
          Code:
          ************************************************************
          Checking input parameters supplied by the user ...
          Validating fastaFileName /data/ngs/annotations/bfast_indexes/hg19.fa. 
          Validating readsFileName /data/ngs/solid/PROJETS/Comp_bowtie_bfast/BFAST/FastQ/reads100000.200.fastq. 
          Validating tmpDir path ./. 
          **** Input arguments look good!
          ************************************************************
          ************************************************************
          Printing Program Parameters:
          programMode:                            [ExecuteProgram]
          fastaFileName:                          /data/ngs/annotations/bfast_indexes/hg19.fa
          mainIndexes                             [Auto-recognizing]
          secondaryIndexes                        [Not Using]
          readsFileName:                          /data/ngs/solid/PROJETS/Comp_bowtie_bfast/BFAST/FastQ/reads100000.200.fastq
          offsets:                                [Using All]
          loadAllIndexes:                         [Not Using]
          compression:                            [Not Using]
          space:                                  [Color Space]
          startReadNum:                           1
          endReadNum:                             2147483647
          keySize:                                [Not Using]
          maxKeyMatches:                          8
          maxNumMatches:                          384
          whichStrand:                            [Both Strands]
          numThreads:                             8
          queueLength:                            250000
          tmpDir:                                 ./
          timing:                                 [Not Using]
          ************************************************************
          Searching for main indexes...
          Found 10 index (10 total files).
          Not using secondary indexes.
          ************************************************************
          Reading in reference genome from /data/ngs/annotations/bfast_indexes/hg19.fa.cs.brg.
          In total read 25 contigs for a total of 3095693983 bases
          ************************************************************
          Reading /data/ngs/solid/PROJETS/Comp_bowtie_bfast/BFAST/FastQ/reads100000.200.fastq into a temp file.
          Will process 100000 reads.
          ************************************************************
          Searching index file 1/10 (index #1, bin #1)...
          Reading index from /data/ngs/annotations/bfast_indexes/hg19.fa.cs.1.1.bif.
          Read index from /data/ngs/annotations/bfast_indexes/hg19.fa.cs.1.1.bif.
          Reads processed: 100000
          Cleaning up index.
          Searching index file 1/10 (index #1, bin #1) complete...
          Found 60065 matches.
          ************************************************************
          Searching index file 2/10 (index #2, bin #1)...
          Reading index from /data/ngs/annotations/bfast_indexes/hg19.fa.cs.2.1.bif.
          and the it crashes with a segfault.

          We generated a core dump but the crash is in a function of libz so we installed the debug version of libz and here is the result: http://pastebin.com/Ae0re589

          So if you have any leads, I would be happy to help and test.

          Best regards
          Last edited by cbarette; 08-02-2010, 07:31 AM.

          Comment


          • #20
            Thank-you for providing a good amount of info to help my debug. Googling the compiler warning, it may be the case that your zlib is buggy in Ubuntu (see my links hinting at that). The function "gzopen64" is declared in zlib to provide 64-bit support, but is not being declared correctly. I am guessing it crashes when trying to read in a compressed index (as shown by the last BFAST status message). In "configure.ac", could you change the "extended_CFLAGS" line to the below and see what happens?
            extended_CFLAGS="-m64 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE";
            The run "sh autogen.sh && ./configure && make".

            Links:

            I've spent the last couple of hours debugging a really strange segfault. Our application stack had a reproduceable crash in libxml2 -- but o...


            Comment


            • #21
              Hi,

              Thanks a lot for your feedback ! With this modification bfast runs perfectly with 8 threads.

              Cheers

              Comment

              Latest Articles

              Collapse

              • seqadmin
                Understanding Genetic Influence on Infectious Disease
                by seqadmin




                During the COVID-19 pandemic, scientists observed that while some individuals experienced severe illness when infected with SARS-CoV-2, others were barely affected. These disparities left researchers and clinicians wondering what causes the wide variations in response to viral infections and what role genetics plays.

                Jean-Laurent Casanova, M.D., Ph.D., Professor at Rockefeller University, is a leading expert in this crossover between genetics and infectious...
                09-09-2024, 10:59 AM
              • seqadmin
                Addressing Off-Target Effects in CRISPR Technologies
                by seqadmin






                The first FDA-approved CRISPR-based therapy marked the transition of therapeutic gene editing from a dream to reality1. CRISPR technologies have streamlined gene editing, and CRISPR screens have become an important approach for identifying genes involved in disease processes2. This technique introduces targeted mutations across numerous genes, enabling large-scale identification of gene functions, interactions, and pathways3. Identifying the full range...
                08-27-2024, 04:44 AM

              ad_right_rmr

              Collapse

              News

              Collapse

              Topics Statistics Last Post
              Started by seqadmin, Today, 06:25 AM
              0 responses
              13 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, Yesterday, 01:02 PM
              0 responses
              12 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 09-18-2024, 06:39 AM
              0 responses
              14 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 09-11-2024, 02:44 PM
              0 responses
              14 views
              0 likes
              Last Post seqadmin  
              Working...
              X