Hi,

Thanks for the reply, sorry about the multiple posts - it kept getting bounced 
so I resubmitted the question. We seem to be having real problems with our 
local install so I'll add it to the list...!

Cheers
David



On 14 Mar 2012, at 18:10, Jennifer Jackson wrote:

> Hi David,
> 
> You question has posted to the list now and we will be getting back to you. 
> It didn't post immediately due to some mail mailman server issues here.
> 
> This looks like a problem that came up on a local instance. Because of that, 
> I am going to send this over to the galaxy-...@bx.psu.edu mailing list. At 
> first glance, this appears to be a problem with the NGS genome indexes used 
> for the target genome. These are the instructions you followed?
> http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup (Bowtie indexes are used 
> for TopHat)
> 
> We will be looking at this more later today, but I wanted to get back to you, 
> so you that you know that this doesn't need to be posted again.
> 
> Thanks!
> 
> Jen
> Galaxy team
> 
> On 3/14/12 6:48 AM, David Matthews wrote:
>> Hi,
>> 
>> JUst running a TopHat job which returned the following error:
>> 
>> Executing: /gpfs/cluster/isys/galaxy/Software/bin/bowtie-inspect 
>> /local/tmp5Ywx45/dataset_942>  ./tophat_out/tmp/dataset_942.fa
>> [Tue Mar 13 12:45:08 2012] Checking for Bowtie
>>      Bowtie version:                  0.12.7.0
>> [Tue Mar 13 12:45:08 2012] Checking for Samtools
>>      Samtools Version: 0.1.18
>> [Tue Mar 13 12:45:08 2012] Generating SAM header for 
>> /local/tmp5Ywx45/dataset_942
>>      format:          fastq
>>      quality scale:   phred33 (default)
>> [Tue Mar 13 12:45:21 2012] Preparing reads
>>      left reads: min. length=56, count=29523921
>>      right reads: min. length=56, count=29543412
>> [Tue Mar 13 13:07:54 2012] Mapping left_kept_reads against dataset_942 with 
>> Bowtie
>> [Tue Mar 13 13:45:26 2012] Processing bowtie hits
>> [Tue Mar 13 14:11:28 2012] Mapping left_kept_reads_seg1 against dataset_942 
>> with Bowtie (1/2)
>> [Tue Mar 13 14:43:27 2012] Mapping left_kept_reads_seg2 against dataset_942 
>> with Bowtie (2/2)
>> [Tue Mar 13 14:57:50 2012] Mapping right_kept_reads against dataset_942 with 
>> Bowtie
>> [Tue Mar 13 15:37:46 2012] Processing bowtie hits
>> [Tue Mar 13 16:04:28 2012] Mapping right_kept_reads_seg1 against dataset_942 
>> with Bowtie (1/2)
>> [Tue Mar 13 16:37:18 2012] Mapping right_kept_reads_seg2 against dataset_942 
>> with Bowtie (2/2)
>> [Tue Mar 13 16:50:40 2012] Searching for junctions via segment mapping
>> Traceback (most recent call last):
>>   File "/gpfs/cluster/isys/galaxy/Software/bin/tophat", line 3063, in<module>
>>     sys.exit(main())
>>   File "/gpfs/cluster/isys/galaxy/Software/bin/tophat", line 3029, in main
>>     user_supplied_deletions)
>>   File "/gpfs/cluster/isys/galaxy/Software/bin/tophat", line 2681, in 
>> spliced_alignment
>>     [maps[initial_reads[left_reads]].unspliced_bwt, 
>> maps[initial_reads[left_reads]].seg_maps[-1]],
>> TypeError: list indices must be integers, not str
>> 
>> Does anyone know what this kind of error is?
>> 
>> Best Wishes,
>> David.
>> 
>> 
>> 
>> __________________________________
>> Dr David A. Matthews
>> 
>> Senior Lecturer in Virology
>> Room E49
>> Department of Cellular and Molecular Medicine,
>> School of Medical Sciences
>> University Walk,
>> University of Bristol
>> Bristol.
>> BS8 1TD
>> U.K.
>> 
>> Tel. +44 117 3312058
>> Fax. +44 117 3312091
>> 
>> d.a.matth...@bristol.ac.uk <mailto:d.a.matth...@bristol.ac.uk>
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> ___________________________________________________________
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