Hi. Newbie here. I'm trying to setup tophat for our local install. I'm
getting the following error when I try to run it. Has anyone seen this
before or have any ideas what I can try to fix it.

Thanks,

Simon

Error in tophat:

[Wed Jun 29 11:54:09 2011] Beginning TopHat run (v1.3.1)
-----------------------------------------------
[Wed Jun 29 11:54:09 2011] Preparing output location ./tophat_out/
[Wed Jun 29 11:54:09 2011] Checking for Bowtie index files
[Wed Jun 29 11:54:09 2011] Checking for reference FASTA file
        Warning: Could not find FASTA file
/var/folders/f1/f1aTv8DnERiCv5ic7O3rlk++-+6/-Tmp-/tmpe7Oa0l/dataset_127234.dat.fa
[Wed Jun 29 11:54:09 2011] Reconstituting reference FASTA file from Bowtie index
Executing: /Volumes/storagepool/oconnorlab/galaxy_dist/bin/bowtie-inspect
/var/folders/f1/f1aTv8DnERiCv5ic7O3rlk++-+6/-Tmp-/tmpe7Oa0l/dataset_127234.dat
> ./tophat_out/tmp/dataset_127234.dat.fa
[Wed Jun 29 11:54:09 2011] Checking for Bowtie
        Bowtie version:                  0.12.5.0
[Wed Jun 29 11:54:09 2011] Checking for Samtools
        Samtools Version: 0.1.7
[Wed Jun 29 11:54:09 2011] Generating SAM header for
/var/folders/f1/f1aTv8DnERiCv5ic7O3rlk++-+6/-Tmp-/tmpe7Oa0l/dataset_127234.dat
[Wed Jun 29 11:54:09 2011] Preparing reads
        format:          fastq
        quality scale:   phred33 (default)
        Left  reads: min. length=17, count=2666051
Warning: short reads (<20bp) will make TopHat quite slow and take
large amount of memory because they are likely to be mapped to too
many places
[Wed Jun 29 11:54:27 2011] Mapping left_kept_reads against
dataset_127234.dat with Bowtie

gzip: stdout: Broken pipe
[Wed Jun 29 11:54:27 2011] Processing bowtie hits
Traceback (most recent call last):
  File "/Volumes/storagepool/oconnorlab/galaxy_dist/bin/tophat", line 2607, in
    sys.exit(main())
  File "/Volumes/storagepool/oconnorlab/galaxy_dist/bin/tophat", line
2566, in main
    user_supplied_deletions)
  File "/Volumes/storagepool/oconnorlab/galaxy_dist/bin/tophat", line
2256, in spliced_alignment
    ref_fasta)
  File "/Volumes/storagepool/oconnorlab/galaxy_dist/bin/tophat", line
2000, in junctions_from_segments
    if left_reads_map != left_seg_maps[0]:
IndexError: list index out of range
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