Alignment problems

[rakscalloni]

Hi!

I'm trying to align my data using Tophat2 and the following files:
genome: Homo_sapiens.GRCh37.75.dna.primary_assembly.fa (from which index files were built using Bowtie)
gtf file: gencode.v19.2wayconspseudos

I'v also tried to align using UCSC available human genome. But, in both cases no "accepted_hits.bam" is generated. Instead of, two folders, named "logs" and "tmp", and a file "prep_reads.info".

Has anybody already had this problem?
Thaks

[GenoMax]

Start looking at the run.log and tophat.log files in the "logs" directory to see if they give a hint as to what error was encountered.

[rakscalloni]

Start looking at the run.log and tophat.log files in the "logs" directory to see if they give a hint as to what error was encountered.

Thank you GenoMax!

There is a problem in the index building. Here is the output message:

[2014-08-18 16:33:32] Building Bowtie index from Homo_sapiens.GRCh37.75.fa
[FAILED]
Error: Couldn't build bowtie index with err = 1

I'm trying to find out what is wrong.