Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Assertion failed error in BFAST localalign

    Hi all, I'm getting the following error when trying to combine bfast and bwa mapped reads. Any suggestions would be appreciated.

    command:
    bfast localalign -f rna.fasta -1 p1.f3.reads.bmf -2 p1.f5.reads.bfm -A 1 -t -U -n 4 > p1.reads.baf

    error:
    Assertion failed: (0 == strcmp(m->readName, r2_name)), function RGMatchesRead_2bmf, file RGMatches.c, line 51.
    Abort trap
    Assertion failed: (0 == strcmp(m->readName, r2_name)), function RGMatchesRead_2bmf, file RGMatches

  • #2
    Looks like your reads are not in the same order within the two files (also p1.f5.reads.bfm should be p1.f5.read.bmf). Take a look at your input FASTQ files to make sure the read names are in the same order.

    Comment


    • #3
      The first and last 100 lines of reads are in the same order. I've renamed the f5 files to bmf (which was a typo when making the files). Could that be responsible?

      Comment


      • #4
        Changed the name and still the same error. How could I ensure that all the names are in the same order?

        Comment


        • #5
          Where are you getting your FASTQ from?

          Comment


          • #6
            From the solid2fastq script that came with bfast+bwa. I made a seperate fastq for each of the F3 and F5 reads rather than paired.

            Comment


            • #7
              Ah, you have to make them together. You cannot convert them unpaired then input them as paired.

              Comment


              • #8
                Oh, I was following the flow from here: http://seqanswers.com/forums/showthr...ight=bfast+bwa

                So, you make the fastq paired, then map using the same fastq file for the f3 and f5 seperately?

                Comment

                Latest Articles

                Collapse

                • seqadmin
                  Advancing Precision Medicine for Rare Diseases in Children
                  by seqadmin




                  Many organizations study rare diseases, but few have a mission as impactful as Rady Children’s Institute for Genomic Medicine (RCIGM). “We are all about changing outcomes for children,” explained Dr. Stephen Kingsmore, President and CEO of the group. The institute’s initial goal was to provide rapid diagnoses for critically ill children and shorten their diagnostic odyssey, a term used to describe the long and arduous process it takes patients to obtain an accurate...
                  12-16-2024, 07:57 AM
                • seqadmin
                  Recent Advances in Sequencing Technologies
                  by seqadmin



                  Innovations in next-generation sequencing technologies and techniques are driving more precise and comprehensive exploration of complex biological systems. Current advancements include improved accessibility for long-read sequencing and significant progress in single-cell and 3D genomics. This article explores some of the most impactful developments in the field over the past year.

                  Long-Read Sequencing
                  Long-read sequencing has seen remarkable advancements,...
                  12-02-2024, 01:49 PM

                ad_right_rmr

                Collapse

                News

                Collapse

                Topics Statistics Last Post
                Started by seqadmin, 12-17-2024, 10:28 AM
                0 responses
                26 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 12-13-2024, 08:24 AM
                0 responses
                42 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 12-12-2024, 07:41 AM
                0 responses
                28 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 12-11-2024, 07:45 AM
                0 responses
                42 views
                0 likes
                Last Post seqadmin  
                Working...
                X