I encountered a problem when trying to mapping RNA-seq reads to the genome.
Fatal error: Tool execution failed
[2015-01-02 07:08:06] Beginning TopHat run (v2.0.9)
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[2015-01-02 07:08:06] Checking for Bowtie
Bowtie version: 2.1.0.0
[2015-01-02 07:08:06] Checking for Samtools
Samtools version: 0.1.18.0
[2015-01-02 07:08:06] Checking for Bowtie index files (genome)..
[2015-01-02 07:08:06] Checking for reference FASTA file
[2015-01-02 07:08:06] Generating SAM header for /galaxy/data/rheMac3/bowtie2_index/rheMac3
format: fastq
quality scale: phred33 (default)
[2015-01-02 07:08:20] Reading known junctions from GTF file
[2015-01-02 07:08:29] Preparing reads
left reads: min. length=101, max. length=101, 3322687 kept reads (9 discarded)
right reads: min. length=101, max. length=101, 3322669 kept reads (27 discarded)
[2015-01-02 07:10:46] Building transcriptome data files..
[2015-01-02 07:11:09] Building Bowtie index from dataset_10111788.fa
[FAILED]
Error: Couldn't build bowtie index with err = 1
The gene annotation file (gff format, then converted to gtf) was downloaded from ENSEMBL.
Does anyone have some suggestions on this issue? Thanks a lot!