X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fruby%2Fscripts%2Fpreprocess.rb;h=2cc1479f4bedc57141954439d5fca9ae728643dd;hb=8f9465b50e205b87c7a01c65c859309293aee085;hp=8829eb622c6d9282d502930c3ab8e40d8f25bc55;hpb=790849e542e581631f0b757becfba72a5f6f1b58;p=jalview.git

diff --git a/forester/ruby/scripts/preprocess.rb b/forester/ruby/scripts/preprocess.rb
index 8829eb6..2cc1479 100644
--- a/forester/ruby/scripts/preprocess.rb
+++ b/forester/ruby/scripts/preprocess.rb
@@ -1,7 +1,7 @@
 #!/usr/local/bin/ruby -w
 
 
-if ( ARGV == nil || ARGV.length != 3 )
+if ( ARGV == nil || ARGV.length != 2 )
   puts( "usage: preprocess.rb <input> <path to Pfam A HMMs>" )         
   exit( -1 )
 end 
@@ -10,7 +10,7 @@ input = ARGV[ 0 ]
 
 pfam = ARGV[ 1 ]
 
-system( "hmmscan --nobias --domtblout " + input + "_hmmscan_260_10 -E 10 " + pfam +  " + input + ".ni.fasta" )
+system( "hmmscan --nobias --domtblout " + input + "_hmmscan_260_10 -E 10 " + pfam + " "  + input + ".ni.fasta" )
 
 system( "hsp " + input + "_hmmscan_260_10 " + input + "_hmmscan_260_10_domain_table" )