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