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SAM to BAM conversion error #45

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Description

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What steps will reproduce the problem?
1. Map reads using this command

PerM /mnt/aspseq/data/sequence/Populus_trichocarpa.v2.fna -1 
/mnt/congenie/asp/sequence_data/solid/asp18/raw/asp18mp_solid_read1.csfasta -2 
/mnt/congenie/asp/sequence_data/solid/asp18/raw/asp18mp_solid_read2.csfasta -U 
5000 -L 100 -v 5 -A -m -s /mnt/congenie/asp/data/perm/ -o 
/mnt/congenie/asp/alignments/perm/asp18mp_U5000_L100_v5.sam

2. Try to convert SAM to BAM

samtools view -bS asp18mp_U5000_L100_v5.sam > asp18mp_U5000_L100_v5.bam

Gives the error

[samopen] SAM header is present: 2518 sequences.
Parse error at line 124592: missing colon in auxiliary data
Aborted

Line 124592 contains

1_1506_394_F3   65  scaffold_2  16894790    255 50M =   16897384    2594    CTTCTAGAACTCGAGATAT
GGGCTGAACACTGAACAGTGTCTGGGCTGCA XJIXXO@?MSKIUXVTPSYWVXROSVUUQPWRMQKH?9CHR8&'(F%!
A9  NM:i:3      CS:Z:C2022322012232223331003212011121201121112220132231 CQ:Z:=</;>;5,
4::28>;<98<>:=<79;<:<6;=68:27)136=&+%,;7)9

Does anyone know what the source of this error is?

Thanks

Original issue reported on code.google.com by n.r.str...@gmail.com on 9 Jun 2011 at 1:09

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