On Mon, Jul 22, 2013 at 10:40 AM, Moritz Juchler
<juch...@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:

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