Error while running Tophat 2.0.11

[SubodhTambat]

Hi everyone,

I have a problem in running tophat 2.0.11 with a 50 bp paired end illumina RNA reads.

I have used following command:

./tophat2 --read-gap-length 2 -r 50 --mate-std-dev 20 -o /home/sandor/Desktop/HD/NGS_analysis/tophat-2.0.11.Linux_x86_64/tophat_out -m 0 -i 70 -I 500000 --max-insertion-length 3 --max-deletion-length 3 -p 4 --report-secondary-alignments --no-coverage-search --segment-length 25 /home/sandor/Desktop/HD/NGS_analysis/tophat-2.0.11.Linux_x86_64/hg19_indexes/hg19 A4EP_GCCAAT_L004_R1_001.fastq_filtered A4EP_GCCAAT_L004_R2_001.fastq_filtered

The output was as follows:

[2014-07-28 10:47:10] Beginning TopHat run (v2.0.11)
-----------------------------------------------
[2014-07-28 10:47:10] Checking for Bowtie
Bowtie version: 2.2.2.0
[2014-07-28 10:47:10] Checking for Samtools
Samtools version: 0.1.18.0
[2014-07-28 10:47:10] Checking for Bowtie index files (genome)..
[2014-07-28 10:47:10] Checking for reference FASTA file
[2014-07-28 10:47:10] Generating SAM header for hg19_indexes/hg19
[2014-07-28 10:48:45] Preparing reads
left reads: min. length=51, max. length=51, 25111234 kept reads (223 discarded)
right reads: min. length=51, max. length=51, 25084880 kept reads (26577 discarded)
[2014-07-28 10:58:49] Mapping left_kept_reads to genome hg19 with Bowtie2
[2014-07-28 11:29:21] Mapping left_kept_reads_seg1 to genome hg19 with Bowtie2 (1/2)
[2014-07-28 11:33:10] Mapping left_kept_reads_seg2 to genome hg19 with Bowtie2 (2/2)
[2014-07-28 11:38:02] Mapping right_kept_reads to genome hg19 with Bowtie2
[2014-07-28 12:09:08] Mapping right_kept_reads_seg1 to genome hg19 with Bowtie2 (1/2)
[2014-07-28 12:12:58] Mapping right_kept_reads_seg2 to genome hg19 with Bowtie2 (2/2)
[2014-07-28 12:18:00] Searching for junctions via segment mapping
[FAILED]

Error: segment-based junction search failed with err =-11
Loading left segment hits...

Appreciate if anyone can help me to resolve this problem.

Thank you.