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 https://main.g2.bx.psu.edu/u/mj--/w/ngs , 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: https://main.g2.bx.psu.edu/u/mj--/w/sample-workflow-whole-exome-sequencing which runs fine ONLINE AT USE GALAXY but produces this error in my local instance 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 online. Best Moritz 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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