Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • BWA 0.6.1 fail to insert infer isize: weird pairing + Segmentation Fault

    Hi all!

    Using the command: bwa sampe refseq.fasta seq_1.aln.sai seq_2.aln.sai seq_1.fastq.gz seq_2.fastq.gz > output.sam , sometimes I get the error that you can see in the title. It looks like this:

    [bwa_sai2sam_pe_core] 5505024 sequences have been processed.
    [bwa_sai2sam_pe_core] convert to sequence coordinate...
    [infer_isize] (25, 50, 75) percentile: (410, 437, 469)
    [infer_isize] fail to infer insert size: weird pairing
    [bwa_sai2sam_pe_core] time elapses: 0.82 sec
    [bwa_sai2sam_pe_core] changing coordinates of 643 alignments.
    [bwa_sai2sam_pe_core] align unmapped mate...
    Segmentation fault

    I did several very similar alignment tasks with BWA, most of them goes through fine, but with a few fastq files this happens. My data is from the 1000genomes, so that shouldn't be the problem I guess.
    Please let me know, if you guys have an idea what's causing this!

    Yours,
    Attila Vikor

  • #2
    The simplest thing is to redo the alignment. If you mistyped a file name somewhere, you might get that result.

    Also, try making the single end .sams separately, and spot check a few pairs of reads, see if thei rcoordiantes and relative orientation make sense. Weird pairing might mean that the reads don't run into each other like they should.

    Comment


    • #3
      Is your genome index made with bwa 0.6.1?
      How much memory do you have ?
      Is the error consistent (reproduceable)?

      Comment


      • #4
        I made the genome index with bwa 0.6.1.
        I have 2GB RAM on this computer, which is not optimal, but the segfaults only happen, if there is a weird pairing before.
        Its consistent.

        I will align the files separately, and see if something comes up.

        Comment


        • #5
          I think you're going to need more that 2GB.
          Try one with 8GB on the problem samples.

          Comment


          • #6
            Apparently the problem was some of the files getting corrupted during downloading. Sorry to have wasted your time with this... Guess I have learned a lesson to always check the MD5 sums when downloading huge files from the internet.

            Comment

            Latest Articles

            Collapse

            • seqadmin
              Strategies for Sequencing Challenging Samples
              by seqadmin


              Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
              03-22-2024, 06:39 AM
            • seqadmin
              Techniques and Challenges in Conservation Genomics
              by seqadmin



              The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

              Avian Conservation
              Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
              03-08-2024, 10:41 AM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, 03-27-2024, 06:37 PM
            0 responses
            13 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-27-2024, 06:07 PM
            0 responses
            11 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-22-2024, 10:03 AM
            0 responses
            53 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-21-2024, 07:32 AM
            0 responses
            69 views
            0 likes
            Last Post seqadmin  
            Working...
            X