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  • error with BWA

    I try to use BWA to align some SOLiD reads.
    1. I build the index
    bwa index -c -a is ecoli.fa

    2. I convert the csfasta and correspond qual file into fastq with solid2fastq.pl supplied by BWA(for test, very small, 50000 reads).

    3. I try to align the reads to the ref
    bwa aln -n 3 -t 4 -M 3 -c ecoli.fa t_ecoli.fastq map.sai
    It gives some strange information as follow:

    lane@LanePC[bwa] bwa aln -n 3 -t 4 -M 3 -c ecoli.fa t_ecoli.fastq map.sai
    (here are some strange symbols)
    (here are some strange symbols too)
    [bwa_aln_core] calculate SA coordinate... 0.03 sec
    [bwa_aln_core] write to the disk... ���� 0.01 sec
    [bwa_aln_core] 25000 sequences have been processed.

    But there is no output file.
    The BWA version is 0.5.9-r16
    Does anyone know why?
    Thanks a lot.

  • #2
    Originally posted by gigigou View Post
    lane@LanePC[bwa] bwa aln -n 3 -t 4 -M 3 -c ecoli.fa t_ecoli.fastq map.sai
    (here are some strange symbols)
    (here are some strange symbols too)
    [bwa_aln_core] calculate SA coordinate... 0.03 sec
    [bwa_aln_core] write to the disk... ���� 0.01 sec
    [bwa_aln_core] 25000 sequences have been processed.
    Those "strange symbols" are your output. You need to direct stdout into the map.sai file

    Try:
    Code:
    bwa aln -n 3 -t 4 -M 3 -c ecoli.fa t_ecoli.fastq [B]>[/B] map.sai

    Comment


    • #3
      I've just started with BWA too.
      I think you need to include a ">" in there somewhere. If you look at the BWA manual the command should be
      bwa aln [-n maxDiff] [-o maxGapO] [-e maxGapE] [-d nDelTail] [-i nIndelEnd] [-k maxSeedDiff] [-l seedLen] [-t nThrds] [-cRN] [-M misMsc] [-O gapOsc] [-E gapEsc] [-q trimQual] <in.db.fasta> <in.query.fq> > <out.sai>

      So, maybe you could try to run
      bwa aln -n 3 -t 4 -M 3 -c ecoli.fa t_ecoli.fastq > map.sai

      I think your strange symbols are the data that should be going into the sai file but withouth the > they are being displayed in the terminal.

      Comment


      • #4
        Originally posted by TonyBrooks View Post
        I've just started with BWA too.
        I think you need to include a ">" in there somewhere. If you look at the BWA manual the command should be
        bwa aln [-n maxDiff] [-o maxGapO] [-e maxGapE] [-d nDelTail] [-i nIndelEnd] [-k maxSeedDiff] [-l seedLen] [-t nThrds] [-cRN] [-M misMsc] [-O gapOsc] [-E gapEsc] [-q trimQual] <in.db.fasta> <in.query.fq> > <out.sai>

        So, maybe you could try to run
        bwa aln -n 3 -t 4 -M 3 -c ecoli.fa t_ecoli.fastq > map.sai

        I think your strange symbols are the data that should be going into the sai file but withouth the > they are being displayed in the terminal.
        YES!
        You are right. I mistaken that ">" as the one quotes the file name which is unnecessary, so I didn't type it.
        But there is another problem: I have 50000 reads, why did it only process 25000 reads? And in the final sam file no read is aligned. All the reads have a flag 4 which corresponds to unmapped.
        Thank you!
        Last edited by gigigou; 09-05-2012, 04:51 PM.

        Comment

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