On Mon, Jul 22, 2013 at 10:40 AM, Moritz Juchler <juchler@stud.uni-heidelberg.de> wrote:
Hey,
now I am having a new problem: Convert SAM to BAM Tool execution generated the following error message:
[samopen] SAM header is present: 93 sequences. Parse error at line 106: sequence and quality are inconsistent /bin/sh: line 1: 27934 Aborted samtools view -bS "/home/trr/galaxy-dist/database/files/000/dataset_17.dat" > "/tmp/tmp-sam_to_bam_converter-ut5Tag/unsorted.bam"
That's bad.
The tool produced the following additional output:
[bam_header_read] EOF marker is absent. The input is probably truncated.
(should I make a new post out of this?)
Which version of samtools? There is a bug in the currently release where that warning is a false alarm: https://github.com/samtools/samtools/issues/18 Peter