Re: [Bio-bwa-help] inconsistent read and CIGAR lengths in 0.7.3a?
Status: Beta
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From: Heng Li <lh...@sa...> - 2013-03-19 00:55:10
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This bug has been fixed in github, r368. It only occurs when the read is bridging three or more adjacent contigs. Therefore it never happens when reads are aligned to the human genome. The fix will be incorporated in all future releases. Thanks, Heng 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... > > > ------------------------------------------------------------------------------ > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_mar_______________________________________________ > Bio-bwa-help mailing list > Bio...@li... > https://lists.sourceforge.net/lists/listinfo/bio-bwa-help -- The Wellcome Trust Sanger Institute is operated by Genome Rese arch Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. |