Thanks a lot Jennifer,
Restart, full paths were OK.
I don't know why but the 2nd version of Tophat (so the tophat tool
available from Galaxy) search indexs in bowtie-index.loc file and not
in bowtie2-index.loc
So, I've added my bowtie2 index paths in bowtie-index. loc file and
tophat run...
But when I want to run tophat with a reference genome from your
history, here is the error message (my reference genome is a GFT file) :
Error in tophat:
[2013-04-11 14:57:12] Beginning TopHat run (v2.0.5)
-----------------------------------------------
[2013-04-11 14:57:12] Checking for Bowtie
Bowtie version: 2.0.0.7
[2013-04-11 14:57:12] Checking for Samtools
Samtools version: 0.1.19.0
[2013-04-11 14:57:13] Checking for Bowtie index files
Error: Could not find Bowtie 2 index files (/tmp/1078173.1.workq/tmpzxEFNK/dataset_6485.*.bt2)
Settings:
blablabla OK.....
Total time for backward call to driver() for mirror index: 00:00:57
TopHat v2.0.5
tophat -p 4 /tmp/1078173.1.workq/tmpzxEFNK/dataset_6485 /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 jeu. avril 11 14:57:18 CEST 2013
Thanks in advance,
Sarah
Jennifer Jackson a écrit :
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
--
--*--
Sarah Maman
INRA - LGC - SIGENAE
http://www.sigenae.org/
Chemin de Borde-Rouge - Auzeville - BP 52627
31326 Castanet-Tolosan cedex - FRANCE
Tel: +33(0)5.61.28.57.08
Fax: +33(0)5.61.28.57.53
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Jennifer Hillman-Jackson
Galaxy Support and Training
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--
--*--
Sarah Maman
INRA - LGC - SIGENAE
http://www.sigenae.org/
Chemin de Borde-Rouge - Auzeville - BP 52627
31326 Castanet-Tolosan cedex - FRANCE
Tel: +33(0)5.61.28.57.08
Fax: +33(0)5.61.28.57.53
--*--