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.comon 9 Jun 2011 at 1:09