Tophat running error 1?

[day_sleeperz]

Hi , I tried to run tophat to align my Solexa reads against the latest GrCh37 assembly. I encounter this error. Could someone help me? Thanks

tophat -i 69 --solexa1.3-quals --coverage-search --fill-gap --microexon-search --GFF Ensembl_h_sapiens.GFF3 h_sapiens_37_asm s_2_sequence_fastq.txt

[Wed Sep 2 16:43:33 2009] Beginning TopHat run (v1.0.11)
-----------------------------------------------
[Wed Sep 2 16:43:33 2009] Preparing output location ./tophat_out/
[Wed Sep 2 16:43:33 2009] Checking for Bowtie index files
[Wed Sep 2 16:43:33 2009] Checking for reference FASTA file
Warning: Could not find FASTA file /home/neuro/Documents/Sonny/bowtie-0.10.1/indexes/h_sapiens_37_asm.fa
[Wed Sep 2 16:43:33 2009] Reconstituting reference FASTA file from Bowtie index
[Wed Sep 2 17:01:26 2009] Checking for Bowtie
Bowtie version: 0.10.1.0
[Wed Sep 2 17:01:27 2009] Checking reads
seed length: 65bp
format: fastq
quality scale: --solexa1.3-quals
[Wed Sep 2 17:03:59 2009] Reading known junctions from GFF file
[Wed Sep 2 17:05:23 2009] Mapping reads against h_sapiens_37_asm with Bowtie
[Wed Sep 2 18:45:28 2009] Joining segment hits
Splitting reads into 2 segments
[Wed Sep 2 18:46:04 2009] Mapping reads against h_sapiens_37_asm with Bowtie
[Wed Sep 2 19:07:29 2009] Mapping reads against h_sapiens_37_asm with Bowtie
[Wed Sep 2 19:26:40 2009] Searching for junctions via segment mapping
[Wed Sep 2 19:28:49 2009] Retrieving sequences for splices
[Wed Sep 2 19:30:36 2009] Indexing splices
Warning: Empty input file
Reference file does not seem to be a FASTA file
[FAILED]
Error: Splice sequence indexing failed with err = 1

[hrajasim]

Figured out yet?

I am running the latest version of tophat 1.3.2 but hit this same error=1 for the first time. I had run tophat 1.2 successfully on 50+ samples. ANy resolution to this issue yet?

I am getting this error only for the second iteration of tophat. I ran first iteration of tophat on each individual sample without the -j option. Then, merged all .juncs.bed files into a master juncs.bed file. Now, when I try tophat with the -j option on each samples (2nd iteration), I get this error.

Thanks for any pointers.

[hrajasim]

Okay this issue was resolved by ensuring a single junctions header at the top and all others removed. Bed needs to be converted into .juncs file using the script bed_to_juncs before feeding into the tophat -j option.