tophat error= -6

[fm_xg]

Hi,
I am new to the bioinformatics field but want to map my RNA-Seq data using TopHat. I've installed tophat and bowtie, however, when i run the programme, there is a error:

[Mon Jun 7 17:12:46 2010] Beginning TopHat run (v1.0.13)
-----------------------------------------------
[Mon Jun 7 17:12:46 2010] Preparing output location ./tophat_out/
[Mon Jun 7 17:12:46 2010] Checking for Bowtie index files
[Mon Jun 7 17:12:46 2010] Checking for reference FASTA file
Warning: Could not find FASTA file rs4779584.fa
[Mon Jun 7 17:12:46 2010] Reconstituting reference FASTA file from Bowtie index
[Mon Jun 7 17:12:46 2010] Checking for Bowtie
Bowtie version: 0.12.5.0
[Mon Jun 7 17:12:46 2010] Checking reads
seed length: 36bp
format: fasta
[Mon Jun 7 17:14:48 2010] Mapping reads against rs4779584 with Bowtie
[Mon Jun 7 17:23:23 2010] Joining segment hits
[Mon Jun 7 17:24:24 2010] Searching for junctions via segment mapping
[FAILED]
Error: segment-based junction search failed with err = -6

I don't know what does "err= -6" mean
I have repeated many times and always meet the same mistake.

[fm_xg]

waitting for help...

[Chrn]

Hi,

Same problem. Testing back and forth showed that for me this was caused by TopHat searching for junctions in a huge index I made (think genome sized in one single contig).

the option --no-novel-juncs allowed it to run. This is not thoroughly tested or confirmed, just relaying what seemed to work for me.

[Chrn]

let me add to that, That doesnt fix the problem completely since the bam file become corrupted by having a contig bigger than a little over 500 Mb

32bit int problem. Be warned =)

[kauralasoo]

For the shake of those finding this thread from Google: In my case, the same error (-6) was caused by lack of memory. Using a computer with larger RAM solved the problem.