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  • honey
    started a topic error running BWA

    error running BWA

    I am running BWA using hg10 on paired end (100XPE) but I am getting error message- Warning: no access to tty (Bad file descriptor).
    Thus no job control in this shell.
    [bwa_aln] 17bp reads: max_diff = 2
    [bwa_aln] 38bp reads: max_diff = 3

    [bwa_aln_core] 168861678 sequences have been processed.
    [bwa_sai2sam_pe_core] convert to sequence coordinate...
    SA-BWT inconsistency: seq_len is not the same. Abort!
    line 20: 22365 Aborted
    [samopen] SAM header is present: 84 sequences.
    [sam_read1] reference 'ID:bwa PN:bwa VN:0.5.9-r16

    27682

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

    What is wrong here and how can I fix it, It is happening with all the files.
    Thanks
    Last edited by honey; 06-01-2012, 09:05 PM.

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