Hello,
I am using GMAP to map cDNA sequences but when I try to convert the SAM files to BAM I get this error:
Line 25706, sequence length 519 vs 499 from CIGAR
Parse error at line 25706: CIGAR and sequence length are inconsistent
I checked this sequence in the SAM file and there is indeed a discrepancy between the length of the sequence and the CIGAR.
This is the line from the SAM file that is causing the problem:
m140206_015639_42149_c100624452550000001823118308061485_s1_p0/61037/33_552_CCS 16 AADN03010840.1 1984 40 5S4M1I1M1I1M1I1M2D1M1I1M1I12M10D27M7I6M6D2M8I3M2D2M2D5M2I5M9D7M2D23M1D8M1I1M1107N8M1I12M1I48M1I56M1I41M1D28M1D6M728N78M5334N1I6M1I43M101N28M1S * 0 0 CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTGTTTTTTTTCTCTTTCTTTTTTTTTTTTCGTTTTTTTCACAGACCAGCGACGTGTTATTACATCTACCGCAGTACAGGTTGTATTTGCCGAGCGCCCTTGGGGTGGGGGCTGCTGTCGGCTGCCCTTGTAGGAGCCAGAATTGCTGCTGCTGCTCAGCGAGGAGGTGGCCGTAGGTGTCCCTCCCAGGGGGCGAGGGGCGCCTGGAGGCAGGGAGAAGAGGCTGGTGTCTCAGGCCGAGTGGCTGAGGGCGCTGACGACTTAAAGAGGAGGCAAAACCACTCCGTCCATAAAGCCGCGACTTCGTGATCCGGTGGATGAGCGTCTGCTCCCCGGCAGAGACATGGCCACGGTGCCGCGGGTCCTGGGCACAGGGGACACTGCGCGGGGGCCCGCGGCTCTCAGGGGCGGCAGCGCCGGGCTCAGCGACCTGCGCCGGCCTCCATGGGTGAGGCGGCC * MD:Z:1GCA0G0C0C^GC1C0C1GCG1G2C2^CAGGCGGGCC2CAGG1GCCG1A1GCACAC3C4GC1G1^AGGGGG5^GT2^TG1TC7^GGTGGTTTG2GC3^GG0T1GT1A1T1C13^G95G78^A28^C83A70C6 NH:i:1 HI:i:1 NM:i:110 SM:i:40 XQ:i:40 X2:i:0 XO:Z:UU XS:A:- PG:Z:M
Has anyone encountered this issue before? What is causing GMAP to produce an incorrect CIGAR for that sequence?
I am using GMAP to map cDNA sequences but when I try to convert the SAM files to BAM I get this error:
Line 25706, sequence length 519 vs 499 from CIGAR
Parse error at line 25706: CIGAR and sequence length are inconsistent
I checked this sequence in the SAM file and there is indeed a discrepancy between the length of the sequence and the CIGAR.
This is the line from the SAM file that is causing the problem:
m140206_015639_42149_c100624452550000001823118308061485_s1_p0/61037/33_552_CCS 16 AADN03010840.1 1984 40 5S4M1I1M1I1M1I1M2D1M1I1M1I12M10D27M7I6M6D2M8I3M2D2M2D5M2I5M9D7M2D23M1D8M1I1M1107N8M1I12M1I48M1I56M1I41M1D28M1D6M728N78M5334N1I6M1I43M101N28M1S * 0 0 CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTGTTTTTTTTCTCTTTCTTTTTTTTTTTTCGTTTTTTTCACAGACCAGCGACGTGTTATTACATCTACCGCAGTACAGGTTGTATTTGCCGAGCGCCCTTGGGGTGGGGGCTGCTGTCGGCTGCCCTTGTAGGAGCCAGAATTGCTGCTGCTGCTCAGCGAGGAGGTGGCCGTAGGTGTCCCTCCCAGGGGGCGAGGGGCGCCTGGAGGCAGGGAGAAGAGGCTGGTGTCTCAGGCCGAGTGGCTGAGGGCGCTGACGACTTAAAGAGGAGGCAAAACCACTCCGTCCATAAAGCCGCGACTTCGTGATCCGGTGGATGAGCGTCTGCTCCCCGGCAGAGACATGGCCACGGTGCCGCGGGTCCTGGGCACAGGGGACACTGCGCGGGGGCCCGCGGCTCTCAGGGGCGGCAGCGCCGGGCTCAGCGACCTGCGCCGGCCTCCATGGGTGAGGCGGCC * MD:Z:1GCA0G0C0C^GC1C0C1GCG1G2C2^CAGGCGGGCC2CAGG1GCCG1A1GCACAC3C4GC1G1^AGGGGG5^GT2^TG1TC7^GGTGGTTTG2GC3^GG0T1GT1A1T1C13^G95G78^A28^C83A70C6 NH:i:1 HI:i:1 NM:i:110 SM:i:40 XQ:i:40 X2:i:0 XO:Z:UU XS:A:- PG:Z:M
Has anyone encountered this issue before? What is causing GMAP to produce an incorrect CIGAR for that sequence?
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