Tophat error

[oiluig87]

I've got this error when i've trying to map my reads against Hg19 genome using gencode v14 as reference GTF file:


[2012-11-10 17:51:33] Beginning TopHat run (v2.0.6)
-----------------------------------------------
[2012-11-10 17:51:33] Checking for Bowtie
Bowtie version: 2.0.2.0
[2012-11-10 17:51:33] Checking for Samtools
Samtools version: 0.1.16.0
[2012-11-10 17:51:33] Checking for Bowtie index files
[2012-11-10 17:51:33] Checking for reference FASTA file
[2012-11-10 17:51:33] Generating SAM header for /home/me/bin/Indexed_Genome
/hg19/hg19
format: fastq
quality scale: phred33 (default)
[2012-11-10 17:51:34] Reading known junctions from GTF file
[2012-11-10 17:52:14] Preparing reads
left reads: min. length=50, max. length=50, 83657898 kept reads (3515 d
iscarded)
[2012-11-10 18:19:37] Creating transcriptome data files..
[2012-11-10 18:21:43] Building Bowtie index from gencode.v14.annotation.fa
[2012-11-10 22:46:26] Mapping left_kept_reads to transcriptome gencode.v14.annot
ation with Bowtie2
[2012-11-11 07:16:33] Resuming TopHat pipeline with unmapped reads
[2012-11-11 07:16:33] Mapping left_kept_reads.m2g_um to genome hg19 with Bowtie2

[FAILED]
Error running bowtie:

What can be the cause of it?
Thanks