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Samtools "is recognized as '*'" "truncated file" error

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  • Samtools "is recognized as '*'" "truncated file" error


    I posted this last week to the samtools thread, but did not receive a reply, so I'm taking another stab at it:

    samtools-0.1.6_x86_64-linux; precompiled version downloaded today

    $ bowtie --version
    bowtie version 0.11.3
    Built on myserver
    Fri Oct 23 13:27:05 MDT 2009
    Compiler: gcc version 4.1.2 20070115 (prerelease) (SUSE Linux)
    Options: -O3
    Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

    $ samtools faidx hs_ref_chr10.fa
    $ cat hs_ref_chr10.fa.fai
    gi|89161187|ref|NC_000010.9|NC_000010 135374737 105 70 71

    Created sam format with bowtie in two ways (behavior described below is the same for both methods):
    1. using -S in bowtie command
    2. using samtools on a bowtie --refout map file

    sam file from method 2 (chromosome 10 only):

    $ cat
    @0-0-3-9833 0 gi|89161187|ref|NC_000010.9|NC_000010 62380535 0 15M * 0 0 GCAAAGGNNATCATT IIIIIIIIIIIIIII NM:i:1 X1:i:5 MD:Z:3A3N0N6
    @0-0-3-9833 16 gi|89161187|ref|NC_000010.9|NC_000010 62382480 0 15M * 0 0 GGGCTANNGCTCATC IIIIIIIIIIIIIII NM:i:1 X1:i:5 MD:Z:7N0N6
    @0-0-6-12817 0 gi|89161187|ref|NC_000010.9|NC_000010 6095909 0 15M * 0 0 TACCACCNNGCCCTT IIIIIIIIIIIIIII NM:i:1 X1:i:265 MD:Z:1A5N0N6
    @0-0-6-12817 16 gi|89161187|ref|NC_000010.9|NC_000010 6097174 0 15M * 0 0 GCATCANNCTCCCGA IIIIIIIIIIIIIII NM:i:1 X1:i:265 MD:Z:7N0N6

    $ samtools view -bt ~/work/hs_ref_chr/hs_ref_chr10.fa.fai -o out.bam
    [sam_header_read2] 1 sequences loaded.
    [sam_read1] reference '16 gi|89161187|ref|NC_000010.9|NC_000010 6097174 0 15M * 0 0 GCATCANNCTCCCGA IIIIIIIIIIIIIII NM:i:1 X1:i:265MD:Z:7N0N6

    ' is recognized as '*'.
    [main_samview] truncated file.

    out.bam is created, but I cannot do anything further with it.

  • #2
    Yeah this is driving me nuts too. Seems google only know that the question has been asked but it doesn't now the answer.


    • #3
      Same issue here, ever find out a solution?


      • #4
        Pretty sure the OP has got past this by now, but for thh32, it looks to me like it's an issue caused by a strange read ID that contains the '@' symbol at the start.

        '@' at the start of a line indicates a comment (header) line in SAM, so it's interpreting your actual reads as part of the header, which then falls over because they aren't in the right format.

        The header should look something like ...

        @HD	VN:1.0	SO:unsorted
        @SQ	SN:chr1	LN:195471971
        @SQ	SN:chr1_GL456210_random	LN:169725
        ... for example, and the reads should then NOT start with an @ ...

        HWI-ST539:109:D14VPACXX:1:1303:19984:9383	65	chr4	147868767	60	99M	=	147868771	0	GTTGGTCAGTAGTACTCGGTTACGCAATTTCCGGATGTAAAGTCTCTAATGGCAGTGGATAGGTGGGGCTAGAGACTCCGGCAACTTTGACCTTTTCAC	[email protected](([email protected][email protected]?;8>>6;='/[email protected]@[email protected])A>[email protected]>BFIIIHCGF<@GEHFA<[email protected]@@	AS:i:495	NM:i:0	XI:f:1	X0:i:1	X1:i:0	XE:i:29	XR:i:99MD:Z:99
        What do the read IDs look like in the fastq file you're aligning?