interproscan run error
I'm getting an error running interproscan at the command line, any ideas what I may have wrong?
version:
InterProScan 5.4-47.0
tmhmm-2.0c
command:
interproscan.sh -i Chromosome_1_protein.fasta -f XML,GFF3
Error
/home/apps/scripts/tmhmm data/tmhmm/2.0/TMHMM2.0.model /home/data/fus_culmorum/036A_Manuscript_Fgraminearum_g ome_reannotation/Chromosome-1_reannotation/publishable/temp/pear.rothamsted.ac.uk_20140714_151840036_fpaz//jobTMHMM-2.0c/0 00000002989_000000003038.fasta -N 1 -PrintNumbers -background 0.081 0.015 0.054 0.061 0.040 0.068 0.022 0.057 0.056 0.093 0.025 0.045 0.049 0.039 0.057 0.068 0.058 0.067 0.013 0.032
Option n is ambiguous (no-d, no-html, no-plot, no-short, no-v1, nod, nohtml, noplot, noshort, nov1)
Unknown option: printnumbers
Unknown option: background
Error on command line at /home/apps/scripts/tmhmm line 32.
UPDATE: WORKED OUT THE PROBLEM:
Had the scripts in our path but not the correct binary.
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What is the exact command that you have used to call InterProscan? And what is the variable 'binary.tmhmm.path' set to? Also, what happends when you just try to run the TMHMM binary against a fasta file?
Managed to work it out, thanks
Had the scripts in our path but not the correct binary.