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>
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> ___________________________________________________________
>> The Galaxy User list should be used for the discussion of
>> Galaxy analysis and other features on the public server
>> at usegalaxy.org.  Please keep all replies on the list by
>> using "reply all" in your mail client.  For discussion of
>> local Galaxy instances and the Galaxy source code, please
>> use the Galaxy Development list:
>> 
>>   http://lists.bx.psu.edu/listinfo/galaxy-dev
>> 
>> To manage your subscriptions to this and other Galaxy lists,
>> please use the interface at:
>> 
>>   http://lists.bx.psu.edu/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to