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