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
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
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