Tophat Segment-based junction error = -9

[UNCKidney]

[Tue Apr 6 12:18:12 2010] Beginning TopHat run (v1.0.13)
-----------------------------------------------
[Tue Apr 6 12:18:12 2010] Preparing output location ./tophat_out/
[Tue Apr 6 12:18:12 2010] Checking for Bowtie index files
[Tue Apr 6 12:18:12 2010] Checking for reference FASTA file
Warning: Could not find FASTA file hg19.fa
[Tue Apr 6 12:18:12 2010] Reconstituting reference FASTA file from Bowtie index
[Tue Apr 6 13:34:32 2010] Checking for Bowtie
Bowtie version: 0.12.3.0
[Tue Apr 6 13:34:32 2010] Checking reads
seed length: 37bp
format: fastq
quality scale: phred33 (default)
[Tue Apr 6 13:47:18 2010] Mapping reads against hg19 with Bowtie
[Tue Apr 6 15:22:25 2010] Joining segment hits
[Tue Apr 6 15:30:27 2010] Searching for junctions via segment mapping
[FAILED]
Error: segment-based junction search failed with err = -9




Not sure what happened and what error 9 means anyone have an idea ? Let me know if I should post any log files, this is my first time using Tophat

[sunnyvu]

From the report you provided, "Warning: Could not find FASTA file hg19.fa", I think you should make sure the index file is ok.

[UNCKidney]

I think it reconstituted it afterwards from the bowtie indexes, should I have downloaded them from EMBL or NCBI instead ? The fasta genome files that is.

[sunnyvu]

Try this one:
When the first running finished, the fasta file was reconstituted into output fold, then move the fasta file from the output fold into index fold.

[sunnyvu]

Try the following:
I guess the file has been created into the output fold. For the next running, try to move the fasta file into the index fold.