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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