Hi Sarah,

Let's try to sort this out. Your problem does not seem to be the same as in the question referenced, but we can see. First - just to double check - since setting up the genome, you have restarted the server? If not, do that first and check to see if that fixes the problem. Basically, you want to follow this checklist and restarting is the final step:
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

If the problem persists, then would you please send a few more details:

1 - full paths* on you system where you keep the .bt2 indexes, sam index, and .fa file. Maybe do an "ls -l" on these dirs so we can check the symbolic links are in place and named correctly.

* as a note, these should be "hard paths" and not symbolic (except for the .fa links), and must have permissions set to be accessible to the "galaxy user"

2 - lines from your bowtie2_indices.loc and sam_fa_indices.loc file for this genome. I may have you double check your builds.txt file later. if this doesn't sounds familiar, it could be the problem, the genome must be in there, too. - see this wiki: http://wiki.galaxyproject.org/Admin/Data%20Integration

3 - full error message you get when you try to run this using a genome in fasta format from your history. It really shouldn't be the same error - something is not right with the settings and a custom genome is not actually being used if that is the case. Give it another try and see what happens, then send that info. This is a bit of a side case, we should get your basic install correct, but knowing how to do this is a good thing and easy to learn.
http://wiki.galaxyproject.org/Support#Custom_reference_genome

It is OK to masked out anything like user names/groups you don't want to share. Please keep on the list in case we need other feedback.

Thanks!

Jen
Galaxy team

On 4/10/13 3:15 AM, Sarah Maman wrote:
Hello,


When I run tophat ("Tophat for Illumina Find splice junctions using RNA-seq data ), the job failed with truncated files. However, index files are available and I get exactly the same error message using built-in index or one of my history.

Tool execution generated the following error message:

Error in tophat:

[2013-04-10 09:17:07] Beginning TopHat run (v2.0.5)
-----------------------------------------------
[2013-04-10 09:17:07] Checking for Bowtie
          Bowtie version:     2.0.0.7
[2013-04-10 09:17:07] Checking for Samtools
        Samtools version:     0.1.19.0
[2013-04-10 09:17:07] Checking for Bowtie index files
Error: Could not find Bowtie 2 index files (/work/galaxy/Danio_rerio.Zv9.62.dna.chromosome.22.fa.*.bt2)


The tool produced the following additional output:

TopHat v2.0.5
tophat -p 4  /work/galaxy/Danio_rerio.Zv9.62.dna.chromosome.22.fa /work/galaxy/database/files/006/dataset_6528.dat
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_index_core] Invalid BAM header.[bam_index_build2] fail to index the BAM file.
Epilog : job finished at mer. avril 10 09:17:12 CEST 2013

In this post (http://dev.list.galaxyproject.org/tophat-for-illumina-looking-in-wrong-directory-for-bowtie2-indexes-tt4658609.html#none), the solution isn't found.

Do you have any idea,
Sarah Maman 
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