Judging from the output, Tophat is able to determine the version of bowtie and call bowtie-inspect to reconstitute the fasta from the index, but can't seem to locate bowtie???? All bowtie executables are in the path as are the samtools.
[Mon Nov 1 14:27:34 2010] Beginning TopHat run (v1.1.2)
-----------------------------------------------
[Mon Nov 1 14:27:34 2010] Preparing output location ./tophat_out/
[Mon Nov 1 14:27:34 2010] Checking for Bowtie index files
[Mon Nov 1 14:27:34 2010] Checking for reference FASTA file
Warning: Could not find FASTA file /sbs/genomes/bowtie/ZmChrBuild_PHIv2.fa
[Mon Nov 1 14:27:34 2010] Reconstituting reference FASTA file from Bowtie index
[Mon Nov 1 14:42:48 2010] Checking for Bowtie
Bowtie version: 0.12.3.0
[Mon Nov 1 14:42:48 2010] Checking for Samtools
[FAILED]
Error: bowtie not found on this system
Any ideas?
Thanks,
Chris
[Mon Nov 1 14:27:34 2010] Beginning TopHat run (v1.1.2)
-----------------------------------------------
[Mon Nov 1 14:27:34 2010] Preparing output location ./tophat_out/
[Mon Nov 1 14:27:34 2010] Checking for Bowtie index files
[Mon Nov 1 14:27:34 2010] Checking for reference FASTA file
Warning: Could not find FASTA file /sbs/genomes/bowtie/ZmChrBuild_PHIv2.fa
[Mon Nov 1 14:27:34 2010] Reconstituting reference FASTA file from Bowtie index
[Mon Nov 1 14:42:48 2010] Checking for Bowtie
Bowtie version: 0.12.3.0
[Mon Nov 1 14:42:48 2010] Checking for Samtools
[FAILED]
Error: bowtie not found on this system
Any ideas?
Thanks,
Chris
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