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  • maq pair end alignment error

    maq pair end alignment error

    maq map out.map re.bfa pair1.bfq pair2.bfq

    -- maq-0.6.3
    [ma_load_reads] loading reads...
    [ma_load_reads] set length of the first read as 41.
    [ma_load_reads] set length of the second read as 41.
    maq: read.cc:59: longreads_t* ma_load_reads(void*, int, void*, int): Assertion `strcmp(name, lr->name[j]) == 0' failed.
    Aborted


    what's the problem?

  • #2
    Any specific reason for using the much older 0.6.3? Sorry not sure of why the error though..
    --
    bioinfosm

    Comment


    • #3
      pair1.fq:
      @seq1_1
      CCCTAAACCCTAAACCCTAAACCCTAAACCTCTGAATCCTT
      +seq1_1
      hhYhhRhhhhhhhhfhh`ThhdhXTaVNWJLKGgcKGgcKG
      @seq2_1
      TAAACCCTAAACCTCTGAATCCTTAATCCCTAAATCCCTAA
      +seq2_1
      hhchh[h]hhhhhVhhhhLhdhhgPPhhUSYOOPQYOOPQQ
      @seq3_1
      AATCCTACATCCATGAATCCCTAAATACCTAATTCCCTAAA
      +seq3_1
      hhhhhhhhhhhhYPhhhhhKhhhTacNhhOF]IIDOF]IID

      pair2.fq:
      @seq1_2
      ACAAATCCTATTTCTTGTGGTTTTCTTTCCTTCACTTAGCT
      +seq1_2
      hhYhhRhhhhhhhhfhh`ThhdhXTaVNWJLKGgcKGgcKG
      @seq2_2
      GTTTTCTTTCCTTCACTTAGCTATGGATGGTTTATCTTCAT
      +seq2_2
      hhchh[h]hhhhhVhhhhLhdhhgPPhhUSYOOPQYOOPQQ
      @seq3_2
      CGAGCACACACACACGGTGGCTATCATCGATCGATCGATGC
      +seq3_2
      hhhhhhhhhhhhYPhhhhhKhhhTacNhhOF]IIDOF]IID

      maq-0.7.1/maq map out.map re.bfa pair1.bfq pair2.bfq

      results:
      seq1_1 ref 1 + 223 1 61 61 61 0 0 1 0
      41 CCCTAAACCCTAAACCCTAAACCCTAAACCTCTGAATCCTT ``Y``R````````````T````XT`VNWJLKG``KG``KG
      seq2_1 ref 18 + 225 1 61 61 61 0 0 1 0
      41 TAAACCCTAAACCTCTGAATCCTTAATCCCTAAATCCCTAA `````[`]`````V````L`````PP``USYOOPQYOOPQQ
      seq3_1 ref 66 + 0 64 61 61 0 0 0 1 0
      41 AATCCTACATCCATGAATCCCTAAATACCTAATTCCCTAAA ````````````YP`````K```T``N``OF]IIDOF]IID
      seq3_1 ref 66 + 0 192 0 0 0 0 0 0 0
      41 CGAGCACACACACACGGTGGCTATCATCGATCGATCGATGC ````````````YP`````K```T``N``OF]IIDOF]IID
      seq1_1 ref 223 + -223 1 61 61 61 0 0 1 0
      41 ACAAATCCTATTTCTTGTGGTTTTCTTTCCTTCACTTAGCT ``Y``R````````````T````XT`VNWJLKG``KG``KG
      seq2_1 ref 242 + -225 1 61 61 61 0 0 1 0
      41 GTTTTCTTTCCTTCACTTAGCTATGGATGGTTTATCTTCAT `````[`]`````V````L`````PP``USYOOPQYOOPQQ

      it's strange! the read id , the mapping position 66

      Comment


      • #4
        You should change your read name to:

        seq1/1, seq1/2
        seq2/1, seq2/2

        MAQ needs to parse the read names to get pairing. Sorry for the inconvenience.

        Comment


        • #5
          Thanks for your reply! Now I get new result:

          seq1/1 ref 1 + 164 1 61 61 61 0 0 1 0 35 C
          CCTAAACCCTAAACCCTAAACCCTAAACCTCTGA ``Y``R````````````T````XT`VNWJLKG``
          seq2/1 ref 40 + 208 1 61 61 61 0 0 1 0 35 T
          TAATCCCTAAATCCCTAAATCTTTAAATCCTACA `````[`]`````V````L`````PP``USYOOPQ
          seq3/1 ref 79 + 0 192 0 0 0 0 0 0 0 35 G
          GGGGGGGGGGGGGCCCCCCCCCCCCCCCCCCCCC ````````````YP`````K```T``N``OF]IID
          seq3/2 ref 79 + 0 64 61 61 0 0 0 1 0 35 T
          GAATCCCTAAATACCTAATTCCCTAAACCCGAAA `]`````V````L`````PP``USYOOPQYOOPQQ
          seq1/2 ref 164 + -164 1 61 61 61 0 0 1 0 35 T
          TTTATGTAATTGCTTATTGTTGTGTGTAGATTTT ````````````T````XT`VNWJLKG``KG``KG
          seq2/2 ref 247 + -208 1 61 61 61 0 0 1 0 35 C
          TTTCCTTCACTTAGCTATGGATGGTTTATCTTCA ````````````YP`````K```T``N``OF]IID

          seq3/2 align on postion 79 , seq3/1 could not aligned but Maq also display it.
          How Maq output pair read alignment?

          Comment

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