Re: [Bio-bwa-help] inconsistent read and CIGAR lengths in 0.7.3a?

[Heng Li <lh...@sa...>]

Could you show an example? Is it possible to given me your reference genome (is it public)? You are aligning to an assembly. It is possible that I have overlooked some corner cases in the presence of many short contigs.

Thanks,

Heng

PS: I guess the total length of contigs is around 268Mb?

On Mar 18, 2013, at 11:50 AM, Douglas G. Scofield wrote:

> Hi, I've been mapping some 100-200 bp single-end reads composed of joined overlapping PE reads.  This error of inconsistent read and CIGAR lengths comes from samtools view -Sb receiving bwa mem output, and has turned up in most mappings of individual lanes.  The sequence length is always a length consistent with our dataset, and the CIGAR length is always large and of the same magnitude.
> 
> ./bwa-0.7.3a/bwa mem -t 8 -M ref.fa joined-reads.fq.gz | samtools view -Sb - > joined.bam
> [M::main_mem] read 542310 sequences (80000143 bp)...
> [samopen] SAM header is present: 10253694 sequences.
> [M::main_mem] read 542074 sequences (80000131 bp)... 
> [M::main_mem] read 542126 sequences (80000106 bp)...
> [M::main_mem] read 541780 sequences (80000144 bp)...
> [M::main_mem] read 542008 sequences (80000233 bp)...
> [M::main_mem] read 541446 sequences (80000252 bp)...
> [M::main_mem] read 541508 sequences (80000213 bp)...
> [M::main_mem] read 541508 sequences (80000083 bp)...
> [M::main_mem] read 541194 sequences (80000233 bp)...
> [M::main_mem] read 541150 sequences (80000155 bp)...
> [M::main_mem] read 541192 sequences (80000148 bp)...
> [M::main_mem] read 541256 sequences (80000178 bp)...
> [M::main_mem] read 541900 sequences (80000175 bp)...
> [M::main_mem] read 541452 sequences (80000147 bp)... 
> Line 17958452, sequence length 192 vs 268435648 from CIGAR
> Parse error at line 17958452: CIGAR and sequence length are inconsistent
> 
> Other examples of the error message, showing a 1-1 mapping from sequence length to CIGAR length:
> 
> Line 21464310, sequence length 185 vs 268435641 from CIGAR
> Line 19254499, sequence length 176 vs 268435632 from CIGAR
> Line 18340511, sequence length 189 vs 268435645 from CIGAR
> Line 11148681, sequence length 182 vs 268435638 from CIGAR
> Line 21119586, sequence length 192 vs 268435648 from CIGAR
> Line 17331580, sequence length 191 vs 268435647 from CIGAR
> Line 10555478, sequence length 182 vs 268435638 from CIGAR
> Line 17958452, sequence length 192 vs 268435648 from CIGAR
> Line 11933371, sequence length 181 vs 268435637 from CIGAR
> Line 13738253, sequence length 179 vs 268435635 from CIGAR
> Line 23942863, sequence length 185 vs 268435641 from CIGAR
> Line 15246868, sequence length 190 vs 268435646 from CIGAR
> Line 14256497, sequence length 191 vs 268435647 from CIGAR
> Line 37720680, sequence length 192 vs 268435648 from CIGAR
> Line 17036331, sequence length 180 vs 268435636 from CIGAR
> Line 10740406, sequence length 186 vs 268435642 from CIGAR
> Line 12467794, sequence length 192 vs 268435648 from CIGAR
> Line 18170858, sequence length 189 vs 268435645 from CIGAR
> Line 10364600, sequence length 191 vs 268435647 from CIGAR
> Line 17908527, sequence length 192 vs 268435648 from CIGAR
> Line 11970932, sequence length 191 vs 268435647 from CIGAR
> Line 19278210, sequence length 186 vs 268435642 from CIGAR
> Line 10920332, sequence length 188 vs 268435644 from CIGAR
> 
> Cheers,
> 
> Doug
> 
> Douglas G. Scofield
> Umeå Plant Sciences Centre
> Umeå University, Umeå Sweden
> dou...@pl...
> dou...@gm...
> 
> 
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