Commit 022bcba2 authored by Sebastien Moretti's avatar Sebastien Moretti
Browse files

Crash prob

parent a491ae22
......@@ -442,7 +442,7 @@ checkAndCleanStderrFiles("$cache/$date.ExonerateError") if ( -e "$cache/$date.Ex
checkOutputFiles();
unlink("$msa") if ( $converted==1 );
unlink 'blast_result.txt';
my @tmpFiles = glob($cache."/${date}*");
my @tmpFiles = glob($cache."/$date*");
if ( exists($tmpFiles[0]) ){
mkdir("$cache/$date.TMP");
move("$_", "$cache/$date.TMP") while(<@tmpFiles>);
......@@ -466,6 +466,8 @@ if ( -s "$originalMSA.cds" || -s "$originalMSA.out" ){
if ( -s "$originalMSA.out");
print " #### File Type= MSA Format= fasta_Exon-Boundaries Name= $originalMSA.boj\n"
if ( -s "$originalMSA.boj" && -s "$originalMSA.cds" && $hideBOJ==0);
unlink "$cache/web_tempo.result";
}
else{
failure();
......@@ -555,9 +557,9 @@ PROTOGENE re-builds the original alignment with nucleotidic information it has g
=over 8
=item version 4.0.0
=item version 4.0.5
=item on Apr 02nd, 2011
=item on Aug 02nd, 2011
=back
......@@ -803,9 +805,9 @@ sub run_BLAST{
if ( -z "$outfile" ){
# BLAST run 2 if no hit with 100% identity and coverage: refseq100 -> nr95 OR nr100 -> nr95
print "run BLAST.. against $blast_param->{'db2'} because there was no acceptable hit against $blast_param->{'db1'}"
print "run BLAST.. against $blast_param->{'db2'} because there was no acceptable hit against $blast_param->{'db1'}\n"
if ( $whatBlast != 1 && $db ne 'nr' );
print "run BLAST.. again, with decreased thresholds, because there was no acceptable hit against $db"
print "run BLAST.. again, with decreased thresholds, because there was no acceptable hit against $db\n"
if ( $whatBlast == 1 || $db eq 'nr' );
system("$webblast_exe -program=blastp -database=$blast_param->{'db2'} $blast_at -infile=$infile -matrix=$blast_param->{'matrix'} -evalue=$blast_param->{'evalue'} -method=geneid -filter=$blast_param->{'filter'} -organism=$species -identity=$blast_param->{'identity2'} -cover=$blast_param->{'cover2'} -hits=$blast_param->{'nbesthits'} -quiet=on -outfile=$outfile");
......
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