1. Thanks, I'll try this out, after you reavealed me which version I should
use :)

2. Originally I had this workflow to start with
, but I at the sam-to-bam conversion I get the "sequences are not currently
available for specified build" error when using "locally cached" and I
can't figure out how to use the reference file hg19.fa without actually
uploading it to Galaxy, because I do not have enough space on the
filesystem where the Galaxy distribution is placed ( /home). The genedata
are all on /genedata. So my question here is: How to use the hg19.fa file
placed on another filesystem then the galaxydist?

3. Thus I searched the web and found this workaround:
which runs fine ONLINE AT USE GALAXY but produces this error in my local

Dataset generation errors
*Dataset 18: Filter SAM on data 7*
Tool execution generated the following error message:

Traceback (most recent call last):
  File "/home/trr/galaxy-dist/tools/samtools/sam_bitwise_flag_filter.py",
line 148, in <module>
    if __name__ == "__main__": main()

  File "/home/trr/galaxy-dist/tools/samtools/sam_bitwise_flag_filter.py",
line 137, in main
    flags = int( fields[flag_col] )
IndexError: list index out of range

So here is my 3rd question: How to solve this error? I didnt find anything


On 22 July 2013 16:54, Peter Cock <p.j.a.c...@googlemail.com> wrote:

> 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:
> https://github.com/samtools/samtools/issues/18
> Peter
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