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revision 1.6, Sun Sep 7 23:38:45 2008 UTC revision 1.7, Mon Sep 8 01:01:18 2008 UTC
# Line 110  Line 110 
110          warn "Missing or zero-size contigs file $contigs_file";          warn "Missing or zero-size contigs file $contigs_file";
111      }      }
112  }  }
113    else {
114        $trouble = 1;
115        print STDERR
116            qq(\nWrong number of mandatory arguments: ),
117            &FIG::flatten_dumper(@ARGV),
118            qq(\n);
119    }
120  die "\n\tusage: $usage\n\n" if $trouble;  die "\n\tusage: $usage\n\n" if $trouble;
121    
122    
# Line 142  Line 149 
149      }      }
150    
151      open(CONTIGS, "<$training_contigs")      open(CONTIGS, "<$training_contigs")
152          || die "could not read-open $training_contigs";          || die "could not read-open training contigs file: $training_contigs";
153    
154      $training_tbl = "$tmp_prefix.train.tbl";      $training_tbl = "$tmp_prefix.train.tbl";
155      open(TRAINING,  ">$training_tbl")  || die "Could not write-open $training_tbl";      open(TRAINING,  ">$training_tbl")  || die "Could not write-open training_tbl file: $training_tbl";
156    
157      my $orf_num = 0;      my $orf_num = 0;
158      my %len_of;     #...Hash storing training contig lens      my %len_of;     #...Hash storing training contig lens
# Line 385  Line 392 
392  #-----------------------------------------------------------------------  #-----------------------------------------------------------------------
393  print STDERR "Re-calling PEGs using trained ICM\n" if $ENV{VERBOSE};  print STDERR "Re-calling PEGs using trained ICM\n" if $ENV{VERBOSE};
394    
395  $fig->run("$glimmer_bin/glimmer3 $glimmeropts -b $tmp_matrix -P $start_freqs $tmp_contig $tmp_model $tmp_prefix");  $fig->run("$glimmer_bin/glimmer3 $glimmeropts -b $tmp_matrix -P $start_freqs $contigs_file $tmp_model $tmp_prefix");
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