===========================================================
.___ __ __
_________________ __ __ __| _/|__|/ |_
/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
##############################################
augustus-3.3.3+dfsg/auxprogs/homGeneMapping/src/genome.cc-843- (SELECT seqname,start,end,type,strand,frame,mult,esource FROM hints NATURAL JOIN \
augustus-3.3.3+dfsg/auxprogs/homGeneMapping/src/genome.cc:844: (SELECT * FROM speciesnames NATURAL JOIN seqnames WHERE speciesname=$1)) ON typeid=type WHERE typename=\"CDS\" OR typename=\"exon\" OR typename=\"intron\";");
augustus-3.3.3+dfsg/auxprogs/homGeneMapping/src/genome.cc-845-
##############################################
augustus-3.3.3+dfsg/auxprogs/utrrnaseq/scripts/data2ucsc.sh-9- line_num_file=`mktemp`
augustus-3.3.3+dfsg/auxprogs/utrrnaseq/scripts/data2ucsc.sh:10: num_lines=`wc -l $1 | cut -f1 -d' ' `
augustus-3.3.3+dfsg/auxprogs/utrrnaseq/scripts/data2ucsc.sh-11- for ((i=1; i<=num_lines; i++)); do
##############################################
augustus-3.3.3+dfsg/auxprogs/utrrnaseq/scripts/test_utr_wrapper.pl-267-# clean up
augustus-3.3.3+dfsg/auxprogs/utrrnaseq/scripts/test_utr_wrapper.pl:268:`cd $stemDir; rm -r $randSubDir;`;
augustus-3.3.3+dfsg/auxprogs/utrrnaseq/scripts/test_utr_wrapper.pl-269-close OUTPUT or die ("Could not close output file $output!\n");
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1065- print LOG "$cmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:1066: system($cmdString)==0 or die("failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1067- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1142- print LOG "$cmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:1143: system($cmdString)==0 or die("failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1144- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1188- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:1189: system("$cmdString")==0 or die("Failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1190- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1246- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:1247: system("$cmdString")==0 or die("Failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1248- $cmdString = "";
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1254- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:1255: system("$cmdString")==0 or die("failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1256- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1273- print LOG "$perlCmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:1274: system("$perlCmdString")==0 or die("failed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1275- print LOG "\# ".(localtime).": rm $hintsfile_temp\n";
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1330- print LOG "$perlCmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:1331: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1332- print LOG "\# ".(localtime).": Alignments from file $prot_seq_files[$i] created.\n";
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1336- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:1337: system("$cmdString")==0 or die("Failed to execute $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1338- }else{
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1345- print LOG "$cmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:1346: system("$cmdString")==0 or die("Failed to execute $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1347- $cmdString = "mv tmp_$prg tmp_$prg$i";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1348- print LOG "$cmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:1349: system("$cmdString")==0 or die("Failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1350- $cmdString = "mv align_$prg align_$prg$i";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1351- print LOG "$cmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:1352: system("$cmdString")==0 or die("Failed to execute: $cmdString!\n\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1353- }else{
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1414- print LOG "$cmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:1415: system($cmdString)==0 or die ("Failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1416- print LOG "Deleting $prot_hints_file_temp\n";
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1421- print LOG "$cmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:1422: system($cmdString)==0 or die ("Failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1423- print LOG "\n\# ".(localtime).": Deleting $prot_hintsfile\n";
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1429- print LOG "$cmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:1430: system($cmdString)==0 or die ("Failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1431- print LOG "\n\# ".(localtime).": Sorting hints file $hintsfile\n";
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1433- print LOG "$cmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:1434: system($cmdString)==0 or die("Failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1435- print LOG "\n\# ".(localtime).": Deleting file $toBeSortedHintsFile\n";
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1453- print LOG "$cmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:1454: system($cmdString)==0 or die ("Failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1455- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1477- print LOG "$perlCmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:1478: system("$perlCmdString")==0 or die("failed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1479- $cmdString = "";
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1485- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:1486: system("$cmdString")==0 or die("Failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1487- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1507- my $thisHintsFile = shift;
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:1508: my @areb2h = `cut -f 2 $thisHintsFile | grep b2h`;
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1509- my $ret = 0;
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1522- print LOG "cut -f 3 $hintsfile | grep -m 1 -v intron\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:1523: my @notIntron = `cut -f 3 $hintsfile | grep -m 1 -v intron`;
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1524- if(not(scalar(@notIntron)==0)){
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1535- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:1536: system($cmdString)==0 or die("Failed to execute: $cmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1537- }else{
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1541- print LOG "$cmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:1542: system($cmdString)==0 or die("Failed to execute: $cmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1543- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1568- print LOG "$perlCmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:1569: system("$perlCmdString")==0 or die ("Failed to execute: $perlCmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1570- $cmdString = "cat $out_file_name >> $final_out_file";
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1572- print LOG $cmdString."\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:1573: system("$cmdString")==0 or die ("Failed to execute: $cmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1574- }else{
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1590- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:1591: system("$cmdString")==0 or die("Failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1592- $string = find("join_mult_hints.pl", $AUGUSTUS_BIN_PATH, $AUGUSTUS_SCRIPTS_PATH, $AUGUSTUS_CONFIG_PATH);
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1600- print LOG "$perlCmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:1601: system("$perlCmdString")==0 or die("Failed to execute: $perlCmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1602- unlink($hintsfile_temp_sort);
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1665- print LOG "$perlCmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:1666: system("$perlCmdString")==0 or die("Failed to execute: $perlCmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1667- $cmdString = "cd $rootDir";
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1698- print LOG "$perlCmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:1699: system("$perlCmdString")==0 or die("Failed to execute: $perlCmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1700- $cmdString = "cd $rootDir";
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1725- print LOG "$perlCmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:1726: system("$perlCmdString")==0 or die("Failed to execute: $perlCmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1727- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1745- print LOG "$perlCmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:1746: system("$perlCmdString")==0 or die("Failed to create new species with new_species.pl, check write permissions in $AUGUSTUS_CONFIG_PATH/species directory! Command was $perlCmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-1747- }else{
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2152- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2153: system("$cmdString")==0 or die("Failed to execute: $cmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2154- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2169- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2170: system("$cmdString")==0 or die("Failed to execute: $cmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2171- open(ERRS, "<", $errorfile) or die("Could not open file $errorfile!\n");
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2188- print LOG "$perlCmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2189: system("$perlCmdString")==0 or die("Failed to execute: $perlCmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2190- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2196- print LOG "$cmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2197: system($cmdString)==0 or die("failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2198- }elsif($trainFromGth){
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2202- print LOG "$cmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2203: system($cmdString)==0 or die("failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2204- }elsif(not($trainFromGth) && $gth2traingenes){
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2208- print LOG "$cmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2209: system($cmdString)==0 or die("failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2210- open(GB, "<", "$otherfilesDir/genbank.initial.gb") or die ("Could not open file $otherfilesDir/genbank.initial.gb!\n");
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2237- if($nice){
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2238: $gb_good_size = `nice grep -c LOCUS $otherfilesDir/genbank.good.gb`;
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2239- }else{
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2240: $gb_good_size = `grep -c LOCUS $otherfilesDir/genbank.good.gb`;
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2241- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2258- print LOG "$perlCmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2259: system("$perlCmdString")==0 or die("Failed to execute: $perlCmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2260- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2273- if($nice){
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2274: $gb_good_size = `nice grep -c LOCUS $otherfilesDir/genbank.good.gb`;
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2275- }else{
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2276: $gb_good_size = `grep -c LOCUS $otherfilesDir/genbank.good.gb`;
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2277- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2290- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2291: system("$cmdString")==0 or die("Failed to execute $cmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2292-
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2297- print LOG "nice grep -c \"exon doesn't end in stop codon\" $errorfile\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2298: $err_stopCodonExcludedFromCDS = `nice grep -c "exon doesn't end in stop codon" $errorfile`;
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2299- }else{
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2300- print LOG "grep -c \"exon doesn't end in stop codon\" $errorfile\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2301: $err_stopCodonExcludedFromCDS = `grep -c "exon doesn't end in stop codon" $errorfile`;
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2302- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2310- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2311: system("$cmdString")==0 or die("Failed to execute $cmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2312- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2342- print LOG "\# ".(localtime).": nice grep -c LOCUS $otherfilesDir/genbank.good.gb\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2343: $gb_good_size = `nice grep -c LOCUS $otherfilesDir/genbank.good.gb`;
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2344- }else{
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2345- print LOG "\# ".(localtime).": grep -c LOCUS $otherfilesDir/genbank.good.gb\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2346: $gb_good_size = `grep -c LOCUS $otherfilesDir/genbank.good.gb`;
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2347- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2358- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2359: system("$cmdString")==0 or die("Failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2360- $target_1 = accuracy_calculator($stdoutfile);
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2371- print LOG "\# ".(localtime).": nice grep -c LOCUS $otherfilesDir/genbank.good.gb\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2372: $gb_good_size = `nice grep -c LOCUS $otherfilesDir/genbank.good.gb`;
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2373- }else{
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2374- print LOG "\# ".(localtime).": grep -c LOCUS $otherfilesDir/genbank.good.gb\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2375: $gb_good_size = `grep -c LOCUS $otherfilesDir/genbank.good.gb`;
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2376- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2395- print LOG "$perlCmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2396: system("$perlCmdString")==0 or die("Failed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2397- print LOG "\# ".(localtime).": parameter optimization finished.\n";
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2406- if($nice){
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2407: $gb_good_size = `nice grep -c LOCUS $otherfilesDir/genbank.good.gb`;
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2408- }else{
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2409: $gb_good_size = `grep -c LOCUS $otherfilesDir/genbank.good.gb`;
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2410- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2421- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2422: system("$cmdString")==0 or die("Failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2423- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2431- print LOG "\# ".(localtime).": nice grep -c LOCUS $otherfilesDir/genbank.good.gb\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2432: $gb_good_size = `nice grep -c LOCUS $otherfilesDir/genbank.good.gb`;
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2433- }else{
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2434- print LOG "\# ".(localtime).": grep -c LOCUS $otherfilesDir/genbank.good.gb\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2435: $gb_good_size = `grep -c LOCUS $otherfilesDir/genbank.good.gb`;
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2436- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2447- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2448: system("$cmdString")==0 or die("Failed to execute: $cmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2449- $target_2 = accuracy_calculator($stdoutfile);
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2460- if($nice){
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2461: $gb_good_size = `nice grep -c LOCUS $otherfilesDir/genbank.good.gb`;
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2462- }else{
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2463: $gb_good_size = `grep -c LOCUS $otherfilesDir/genbank.good.gb`;
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2464- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2475- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2476: system("$cmdString")==0 or die("failed to execute: $cmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2477- print LOG "\# ".(localtime).": etraining with CRF finished.\n";
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2484- if($nice){
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2485: $gb_good_size = `nice grep -c LOCUS $otherfilesDir/genbank.good.gb`;
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2486- }else{
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2487: $gb_good_size = `grep -c LOCUS $otherfilesDir/genbank.good.gb`;
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2488- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2499- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2500: system("$cmdString")==0 or die("Failed to execute: $cmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2501- $target_3 = accuracy_calculator($stdoutfile);
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2515- print LOG "$cmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2516: system("$cmdString")==0 or die("failed to execute: $cmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2517- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2523- print LOG "$cmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2524: system("$cmdString")==0 or die("Failed to execute: $cmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2525- print LOG "$cmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2526- $cmdString = "cp $AUGUSTUS_CONFIG_PATH/species/$species/$_".".HMM $AUGUSTUS_CONFIG_PATH/species/$species/$_";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2527: system("$cmdString")==0 or die("Failed to execute: $cmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2528- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2541- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2542: system("$cmdString")==0 or die("Failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2543- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2571- print LOG "$perlCmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2572: system("$perlCmdString")==0 or die("Failed to execute: $perlCmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2573- if($nice){
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2574- print LOG "\# ".(localtime).": nice find $otherfilesDir -name \"genome.split.*\"\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2575: @genome_files = `nice find $otherfilesDir -name "genome.split.*"`;
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2576- }else{
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2577- print LOG "\# ".(localtime).": find $otherfilesDir -name \"genome.split.*\"\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2578: @genome_files = `find $otherfilesDir -name "genome.split.*"`;
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2579- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2604- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2605: system("$cmdString")==0 or die("Failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2606- $pm->finish;
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2632- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2633: system("$cmdString")==0 or die("Failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2634- $pm->finish;
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2650- print LOG "$cmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2651: system("$cmdString")==0 or die("Failed to execute $cmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2652- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2659- print LOG "$perlCmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2660: system("$perlCmdString")==0 or die("Failed to execute $perlCmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2661- for(my $idx = 1; $idx <= scalar(@genome_files); $idx++){
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2676- print LOG "$cmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2677: system("$cmdString")==0 or die("Failed to execute $cmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2678- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2685- print LOG "$perlCmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2686: system("$perlCmdString")==0 or die("Failed to execute $perlCmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2687- for(my $idx = 1; $idx <= scalar(@genome_files); $idx++){
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2701- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2702: system("$cmdString")==0 or die("Failed to execute: $cmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2703- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2710- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2711: system("$cmdString")==0 or die("Failed to execute: $cmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2712- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2729- print LOG "$perlCmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2730: system("$perlCmdString")==0 or die("Failed to execute: $perlCmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2731-}
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2747- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2748: system("$cmdString")==0 or die("Failed to execute: $cmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2749- if($gff3){
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2759- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2760: system("$cmdString")==0 or die("Failed to execute: $cmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2761- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2770- print LOG "\# ".(localtime).": nice find $otherfilesDir -empty\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2771: @files = `nice find $otherfilesDir -empty`;
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2772- }else{
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2773- print LOG "\# ".(localtime).": find $otherfilesDir -empty\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2774: @files = `find $otherfilesDir -empty`;
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2775- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2814- $augpath = "$AUGUSTUS_BIN_PATH/augustus";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2815: if(system("$augpath > /dev/null 2> /dev/null") != 0){ # see autoAug.pl
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2816- if(! -f $augpath){ # see autoAug.pl
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2828- # check whether bamtools is installed
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2829: if(system("which $BAMTOOLS_BIN_PATH/bamtools > /dev/null") != 0){
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2830- $prtStr = "\# ".(localtime).": ERROR: bamtools not installed. Please install it first.\n";
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2838- $etrainpath = "$AUGUSTUS_BIN_PATH/etraining";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:2839: if(system("$etrainpath > /dev/null 2> /dev/null") != 0){
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-2840- if(! -f $etrainpath){
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3189- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:3190: system("$cmdString")==0 or die("Failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3191- open(SAM, "<", $samHeaderFile) or die("Could not open SAM file $samHeaderFile!\n");
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3265- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:3266: system("$cmdString")==0 or die("failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3267- open(SAM, "<", $samFile) or die("Could not open SAM file $samFile!\n");
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3287- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:3288: system("$cmdString")==0 or die("failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3289- print LOG "\# ".(localtime).": Deleting $samFile_new\n";
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3298- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:3299: system("$cmdString")==0 or die("failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3300- print LOG "\# ".(localtime).": Deleting $samFile\n";
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3416- print LOG "$perlCmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:3417: system("$perlCmdString")==0 or die("Failed to execute: $perlCmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3418- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3438- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:3439: system("$cmdString")==0 or die("Failed to execute: $cmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3440-}
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3547- print LOG "\n$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:3548: system("$cmdString") or die ("Failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3549- }else{
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3552- print LOG "$cmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:3553: system($cmdString)==0 or die("Failed to exectute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3554- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3561- print LOG "\n$cmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:3562: system("$cmdString")==0 or die ("Failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3563- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3572- print LOG "\n$cmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:3573: system("$cmdString")==0 or die ("Failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3574- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3592- print LOG "\n$cmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:3593: system($cmdString)==0 or die("Failed not execute $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3594- print LOG "\nrm tr.lst\n";
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3597- print LOG "\n$cmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:3598: system($cmdString)==0 or die("Failed not execute $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3599- open(TR, "tr.lst") or die ("Can not open tr.lst!\n");
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3616- print LOG "\n$cmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:3617: system($cmdString)==0 or die("Failed not execute $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3618- open(GENES, "<", "genes.gtf_temp") or die ("Can not open the file genes.gtf_temp!\n");
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3632- print LOG "\n$cmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:3633: system($cmdString)==0 or die("Failed not execute $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3634- $string = find("gff2gbSmallDNA.pl", $AUGUSTUS_BIN_PATH, $AUGUSTUS_SCRIPTS_PATH, $AUGUSTUS_CONFIG_PATH);
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3636- print LOG "\n$perlCmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:3637: system("$perlCmdString")==0 or die ("Failed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3638- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3675- print LOG "\nperlCmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:3676: system("$perlCmdString")==0 or die ("Failed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3677- $perlCmdString="perl $string genbank.good.gb.test $n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3678- print LOG "\n$perlCmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:3679: system("$perlCmdString")==0 or die ("Failed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3680- my $delete;
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3691- print LOG "\n$cmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:3692: system("$cmdString")==0 or die("Failed to execute: $cmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3693- # count how many genes are contained in train.gb
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3736- print LOG "\n$perlCmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:3737: system("$perlCmdString")==0 or die ("Failed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3738- $cmdString = "cat cdsonly.gb train.utronly.gb > onlytrain.gb";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3739- print LOG "\n$cmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:3740: system("$cmdString")==0 or die("failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3741- # changing UTR parameters in species config file to "on"
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3753- print LOG "Copying utr metaparameter template file:\n$cmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:3754: system("$cmdString")==0 or die ("Failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3755- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3760- print LOG "Running \"$perlCmdString\"...";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl:3761: system("$perlCmdString")==0 or die ("Failed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/braker.pl-3762- }else{
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl-209- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl:210: system("$cmdString")==0 or die("failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl-211- make_path($tmpDir);
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl-233- $cmdString = "ln -s $genome_file $linkName";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl:234: system($cmdString)==0 or die ("Failed to execute $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl-235- print LOG "\# ".(localtime).": $cmdString\n";
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl-265- $cmdString = "ln -s $prot_file $linkName";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl:266: system($cmdString)==0 or die ("Failed to execute $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl-267- print LOG "\# ".(localtime).": $cmdString\n";
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl-449- $cmdString = "rm -r $alignDir";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl:450: system($cmdString)==0 or die("Failed to execute $cmdString\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl-451- make_path($alignDir);
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl-493- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl:494: system("$cmdString")==0 or die("failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl-495- $pm->finish;
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl-535- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl:536: system("$cmdString")==0 or die("failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl-537- $pm->finish;
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl-555- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl:556: system("$cmdString")==0 or die("failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl-557- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl-582- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl:583: system("$cmdString")==0 or die("failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl-584-}
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl-603- print LOG "\# ".(localtime).": $cmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl:604: system("$cmdString")==0 or die ("failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl-605- $protein = $proteinStemPath."/".$proteinPath[(scalar(@proteinPath)-1)];
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl-618- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl:619: system("$cmdString")==0 or die("failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl-620- $cmdString = "rm -r $proteinStemPath";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl-621- print LOG "\# ".(localtime).": $cmdString\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl:622: system ("$cmdString")==0 or die("failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl-623-}
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl-644- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl:645: system("$cmdString")==0 or die("failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl-646- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl-654- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl:655: system("$cmdString")==0 or die("failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl-656- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl-669- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl:670: system("$cmdString")==0 or die("failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl-671- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl-680- print LOG "\# OUTPUT OF makblk.pl STARTING #\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl:681: system("$cmdString")==0 or die("failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl-682- }
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl-696- print LOG "$cmdString\n\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl:697: system("$cmdString")==0 or die("failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl-698-}
##############################################
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl-857- print LOG "NEXT STEP: delete empty files\n";
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl:858: my @files = `find $alignDir -empty`;
augustus-3.3.3+dfsg/docs/tutorial2018/BRAKER_v2.0.4+/startAlign.pl-859- print LOG "\# ".(localtime).": delete empty files\n";
##############################################
augustus-3.3.3+dfsg/scripts/aa2nonred.pl-179- if($CPU > 1){
augustus-3.3.3+dfsg/scripts/aa2nonred.pl:180: system("$DIAMOND_PATH/diamond makedb --in $tempdbname -d $tempdbname --threads $CPU");
augustus-3.3.3+dfsg/scripts/aa2nonred.pl-181- }else{
augustus-3.3.3+dfsg/scripts/aa2nonred.pl:182: system("$DIAMOND_PATH/diamond makedb --in $tempdbname -d $tempdbname --threads 1");
augustus-3.3.3+dfsg/scripts/aa2nonred.pl-183- }
##############################################
augustus-3.3.3+dfsg/scripts/aa2nonred.pl-185- ## NCBI blast
augustus-3.3.3+dfsg/scripts/aa2nonred.pl:186: system("$BLAST_PATH/makeblastdb -in $tempdbname -dbtype prot -parse_seqids -out $tempdbname");
augustus-3.3.3+dfsg/scripts/aa2nonred.pl-187-}
##############################################
augustus-3.3.3+dfsg/scripts/aa2nonred.pl-190- if($diamond){
augustus-3.3.3+dfsg/scripts/aa2nonred.pl:191: system("$DIAMOND_PATH/diamond blastp --db $tempdbname --outfmt 0 --query $tempdbname --out $tempoutfile")
augustus-3.3.3+dfsg/scripts/aa2nonred.pl-192-
augustus-3.3.3+dfsg/scripts/aa2nonred.pl-193- }else{
augustus-3.3.3+dfsg/scripts/aa2nonred.pl:194: system("$BLAST_PATH/blastp -query $tempdbname -db $tempdbname > $tempoutfile");
augustus-3.3.3+dfsg/scripts/aa2nonred.pl-195- }
##############################################
augustus-3.3.3+dfsg/scripts/aa2nonred.pl-197- if($diamond){
augustus-3.3.3+dfsg/scripts/aa2nonred.pl:198: system("$DIAMOND_PATH/diamond blastp --db $tempdbname --outfmt 0 --query $tempdbname --threads $CPU --out $tempoutfile");
augustus-3.3.3+dfsg/scripts/aa2nonred.pl-199- }else{
##############################################
augustus-3.3.3+dfsg/scripts/aa2nonred.pl-202- my $pid = $pm->start and next;
augustus-3.3.3+dfsg/scripts/aa2nonred.pl:203: system("$BLAST_PATH/blastp -query $tempdbname -db $tempdbname > $_.blastout");
augustus-3.3.3+dfsg/scripts/aa2nonred.pl-204- $pm->finish;
##############################################
augustus-3.3.3+dfsg/scripts/aa2nonred.pl-207- foreach ( @splitFiles ) {
augustus-3.3.3+dfsg/scripts/aa2nonred.pl:208: system("cat $_.blastout >> $tempoutfile");
augustus-3.3.3+dfsg/scripts/aa2nonred.pl-209- }
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-212- print "3 $perlCmdString\n" if ($verbose>2);
augustus-3.3.3+dfsg/scripts/autoAug.pl:213: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-214- unless(-e $genome_clean){die("Clean genome file $genome_clean does not exist!\n");}
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-319- print "3 ln -s $genome genome.fa\n" if($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAug.pl:320: system("ln -s $genome genome.fa")==0 or die("\nfailed to execute ln -s $genome genome.fa\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-321- }
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-365- print "3 ln -fs $fasta_cdna transcripts.fasta\n" if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAug.pl:366: system("ln -fs $fasta_cdna transcripts.fasta")==0 or die ("failed to execute: ln -fs $fasta_cdna transcripts.fasta\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-367- }
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-372- print "2 Running $perlCmdString ..." if ($verbose>=2);
augustus-3.3.3+dfsg/scripts/autoAug.pl:373: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-374- print " Finished!\n" if ($verbose>=2);
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-385- print "3 $cmdString\n" if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAug.pl:386: system("$cmdString")==0 or die ("failed to execute: $cmdString\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-387-
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-404- print "3 $cmdString\n" if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAug.pl:405: system("$cmdString")==0 or die ("failed to execute: $cmdString\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-406- print "3 Adjusted alignAssembly.config\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-416- print "3 $cmdString\n" if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAug.pl:417: system("$cmdString")==0 or die("\nfailed to execute $cmdString\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-418-
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-462-
augustus-3.3.3+dfsg/scripts/autoAug.pl:463: system("$perlCmdString")==0 or die ("$abortString");
augustus-3.3.3+dfsg/scripts/autoAug.pl-464- print " Finished\n" if ($verbose>=2);
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-473- print "2 Running $perlCmdString ..." if ($verbose>=2);
augustus-3.3.3+dfsg/scripts/autoAug.pl:474: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-475- print " Finished\n" if ($verbose>=2);
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-487- print "3 Deleting $file\n" if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAug.pl:488: system("$perlCmdString");
augustus-3.3.3+dfsg/scripts/autoAug.pl-489- }
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-501- print "3 $cmdString 1> pasa.complete.lst\n" if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAug.pl:502: system("$cmdString 1> pasa.complete.lst")==0 or die("\nfailed to execute $cmdString\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-503- if (! -e "pasa.complete.lst" || -z "pasa.complete.lst"){
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-507- print "2 Running \"$cmdString\" ..." if ($verbose>=2);
augustus-3.3.3+dfsg/scripts/autoAug.pl:508: system("$cmdString")==0 or die("\nfailed to execute $cmdString\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-509- print " Finished!\n" if ($verbose>=2);
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-516- print "2 Running \"$cmdString\" ..." if ($verbose >=2);
augustus-3.3.3+dfsg/scripts/autoAug.pl:517: system("$cmdString")==0 or die("\nfailed to execute $cmdString\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-518- print " Finished!\n" if ($verbose >=2);
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-552- print "3 $perlCmdString\n" if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAug.pl:553: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-554-
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-569- print "3 $cmdString\n" if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAug.pl:570: system("$cmdString")==0 or die ("failed to execute: $cmdString\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-571-
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-576- print "3 $cmdString\n" if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAug.pl:577: system("$cmdString")==0 or die ("failed to execute: $cmdString\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-578-
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-583- # $cmdString="mv $trainDir/pasa/trainingSetComplete.gb $trainDir/training/trainingSetComplete.gb";
augustus-3.3.3+dfsg/scripts/autoAug.pl:584: # system("$cmdString")==0 or die("\nfailed to move trainingSetComplete.gb to $trainDir/training\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-585- print "3 cd $trainDir/training\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-588- print "3 Running \"$cmdString\" ... " if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAug.pl:589: system("$cmdString")==0 or die("\nfailed to execute: $cmdString\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-590- print " Finished!\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-599- chdir "$genericPathTrain" or die ("Can not chdir to $genericPathTrain.\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl:600: system('cat generic_parameters.cfg | perl -pe \'s/(stopCodonExcludedFromCDS ).*/$1false /\' > '."${species}_generic_parameters.cfg")==0 or die ("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-601- print "3 Set value of \"stopCodonExcludedFromCDS\" in ${species}_generic_parameters.cfg to \"false\"\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-605- print "3 Running \"$cmdString\" ... " if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAug.pl:606: system("$cmdString")==0 or die("\nfailed to execute: $cmdString\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-607- print " Finished!\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-616- print "3 $cmdString\n" if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAug.pl:617: system("$cmdString")==0 or die ("failed to execute: $cmdString\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-618-
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-623- print "3 Running $perlCmdString ...\n" if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAug.pl:624: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-625-
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-639- print "3 Running $perlCmdString ..." if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAug.pl:640: system("$perlCmdString")==0 or die("\nfailed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-641- print " Finished!\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-654- print "3 Running $perlCmdString ..." if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAug.pl:655: system("$perlCmdString")==0 or die("\nfailed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-656- print " Finished!\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-660- print "3 Running $cmdString ..." if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAug.pl:661: system("$cmdString")==0 or die("\nfailed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-662- print " Finished!\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-671- if (!uptodate([$fasta_cdna], ["cdna.fa"])){
augustus-3.3.3+dfsg/scripts/autoAug.pl:672: system("ln -fs $fasta_cdna cdna.fa")==0 or die ("failed to execute: ln -fs $fasta_cdna cdna.fa");
augustus-3.3.3+dfsg/scripts/autoAug.pl-673- }
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-682-
augustus-3.3.3+dfsg/scripts/autoAug.pl:683: system("$cmdString")==0 or die("$abortString");
augustus-3.3.3+dfsg/scripts/autoAug.pl-684- print "Finished!\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-701-
augustus-3.3.3+dfsg/scripts/autoAug.pl:702: if (system("$cmdString") != 0) {
augustus-3.3.3+dfsg/scripts/autoAug.pl-703- print "WARNING: Could not successfully find and run pslCDnaFilter. Please install this program.\n";
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-711- print "3 Running $perlCmdString ..." if ($verbose>3);
augustus-3.3.3+dfsg/scripts/autoAug.pl:712: system("$perlCmdString")==0 or die("\nFailed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-713- print " Finished!\n" if ($verbose>3);
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-720- print "2 Running $perlCmdString ..." if ($verbose>=2);
augustus-3.3.3+dfsg/scripts/autoAug.pl:721: system("$perlCmdString")==0 or die("\nfailed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-722- print " Finished!\n" if ($verbose>=2);
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-731- print "2 Running $perlCmdString ..." if ($verbose>=2);
augustus-3.3.3+dfsg/scripts/autoAug.pl:732: system("$perlCmdString")==0 or die("\nfailed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-733- print " Finished!\n" if ($verbose>=2);
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-738- print "3 Running $perlCmdString.\n" if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAug.pl:739: system("$perlCmdString")==0 or die("\nfailed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-740- rename("../hints/hints.E.gff.temp","../hints/hints.E.gff");
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-761- print "\n2 $perlCmdString\n" if ($verbose>=2);
augustus-3.3.3+dfsg/scripts/autoAug.pl:762: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-763-
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-800- print "2 $perlCmdString\n" if ($verbose>=2);
augustus-3.3.3+dfsg/scripts/autoAug.pl:801: system("$perlCmdString")==0 or die("\nfailed to execute $perlCmdString\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-802-
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-862- chdir $positionWD;
augustus-3.3.3+dfsg/scripts/autoAug.pl:863: system("$perlCmdString")==0 or die ("$abortString");
augustus-3.3.3+dfsg/scripts/autoAug.pl-864-
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-901- print "2 $perlCmdString ...\n" if ($verbose>1);
augustus-3.3.3+dfsg/scripts/autoAug.pl:902: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-903-
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-932- print "\n2 $perlCmdString\n" if ($verbose>=2);
augustus-3.3.3+dfsg/scripts/autoAug.pl:933: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-934-
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-956- }
augustus-3.3.3+dfsg/scripts/autoAug.pl:957: system("mkdir -p $summary_dir")==0 or die("\nCould not create directory $summary_dir.\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-958-
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-967- chdir "gbrowse";
augustus-3.3.3+dfsg/scripts/autoAug.pl:968: system ("ln -sf $genome genome.fa") if (!uptodate([$genome], ["genome.fa"]));
augustus-3.3.3+dfsg/scripts/autoAug.pl-969-
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-971- $cmdString = "cp $rootDir/seq/contigs.gff contigs.gff";
augustus-3.3.3+dfsg/scripts/autoAug.pl:972: system("$cmdString")==0 or die("\nfailed to execute: $cmdString\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-973-
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-975- $cmdString = "ln -sf $rootDir/cdna/cdna.gbrowse cdna.gbrowse";
augustus-3.3.3+dfsg/scripts/autoAug.pl:976: system("$cmdString")==0 or die("\nfailed to execute: $cmdString\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-977- }
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-980- $cmdString = "ln -sf $fasta_cdna cdna.fa";
augustus-3.3.3+dfsg/scripts/autoAug.pl:981: system("$cmdString")==0 or die("\nfailed to execute: $cmdString\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-982- }
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-991- print "3 $cmdString\n" if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAug.pl:992: system("$cmdString")==0 or die ("Could not execute $cmdString");
augustus-3.3.3+dfsg/scripts/autoAug.pl-993- }
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-1000- $cmdString="ln -sf $rootDir/hints/hints.E.gff hints.E.gff";
augustus-3.3.3+dfsg/scripts/autoAug.pl:1001: system("$cmdString")==0 or die("\nfailed to execute: $cmdString\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-1002- print "3 $cmdString\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-1004- $cmdString="ln -sf $hints hints.E.gff";
augustus-3.3.3+dfsg/scripts/autoAug.pl:1005: system("$cmdString")==0 or die("\nfailed to execute: $cmdString\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-1006- print "3 $cmdString\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-1021- print "3 $cmdString\n" if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAug.pl:1022: system("$cmdString")==0 or die ("Could not execute $cmdString");
augustus-3.3.3+dfsg/scripts/autoAug.pl-1023- }
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-1029-
augustus-3.3.3+dfsg/scripts/autoAug.pl:1030: system("$cmdString")==0 or die("\nfailed to execute: $cmdString\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-1031- print "3 $cmdString\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-1039- print "3 $cmdString\n" if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAug.pl:1040: system("$cmdString")==0 or die ("failed to execute: $cmdString\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-1041- }
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-1048- "find $rootDir/autoAugTrain -name \"*.gb.*\" | grep -v .gb.lst >> tempgbn")){
augustus-3.3.3+dfsg/scripts/autoAug.pl:1049: system("$_")==0 or die("\nfailed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-1050- print "3 $_\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-1057- $cmdString="ln -fs $1$2 $2"."_another";
augustus-3.3.3+dfsg/scripts/autoAug.pl:1058: system("$cmdString")==0 or die("\nfailed to execute: $cmdString\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-1059- print "3 $cmdString\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-1062- $cmdString="ln -s $1$2 $2";
augustus-3.3.3+dfsg/scripts/autoAug.pl:1063: system("$cmdString")==0 or die("\nfailed to execute: $cmdString\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-1064- print "3 $cmdString\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/scripts/autoAug.pl-1067- print "3 rm tempgbn\n" if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAug.pl:1068: system("rm tempgbn")==0 or die die("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAug.pl-1069-
##############################################
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-148-for (my $i=1; $i <= $splitN; $i++){
augustus-3.3.3+dfsg/scripts/autoAugPred.pl:149: push @dopreds, $i if (!uptodate(["$workDir/shells/aug$i"], ["$workDir/shells/aug$i.out"]) || !`tail aug$i.out | grep command | wc -l`);
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-150-}
##############################################
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-164- print "2 running aug$i\n" if ($verbose >= 2);
augustus-3.3.3+dfsg/scripts/autoAugPred.pl:165: system ("./aug$i");
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-166- }
##############################################
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-209- if (!uptodate(["$hints"],["$positionWD/hints/hints.gff"])){
augustus-3.3.3+dfsg/scripts/autoAugPred.pl:210: system("ln -fs $hints $positionWD/hints/hints.gff")==0 or die ("Failed to create hints link.\n");
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-211- }
##############################################
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-225- # if (!uptodate([$genome], ["$positionWD/seq/genome.fa"])){
augustus-3.3.3+dfsg/scripts/autoAugPred.pl:226: # system("ln -fs $genome $$positionWD/seq/genome.fa")==0 or die ("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-227- # print("3 Created a link to $genome with the name genome.fa under $positionWD/seq/\n") if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-244- # calculate minsize
augustus-3.3.3+dfsg/scripts/autoAugPred.pl:245: my $minsize = `grep -v ">" $genome | wc -c`;
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-246- $minsize = int($minsize/$nodeNum)+1;
##############################################
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-250- print "3 $perlCmdString ..." if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAugPred.pl:251: system("$perlCmdString")==0 or die ("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-252- print "2 The splited fasta files have been placed under $splitDir\n" if ($verbose>=2);
##############################################
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-256-
augustus-3.3.3+dfsg/scripts/autoAugPred.pl:257: my $splitN = `ls $splitDir/*.fa | wc -l`;
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-258- chomp $splitN;
##############################################
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-279- close AUG;
augustus-3.3.3+dfsg/scripts/autoAugPred.pl:280: system("chmod +x aug$i")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-281- }
##############################################
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-344- print "3 rm $out\n" if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAugPred.pl:345: system("rm $out")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-346- }
##############################################
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-351- print "3 cat aug$i.out >> $out\n" if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAugPred.pl:352: system("cat aug$i.out >> $out")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugPred.pl:353: if (`tail aug$i.out | grep command | wc -l` != 1){
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-354- $notfinished++;
##############################################
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-363- print "3 cat $out | $string > augustus.gff\n" if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAugPred.pl:364: system("cat $out | $string > augustus.gff")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-365-
##############################################
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-369- print "3 $perlCmdString\n" if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAugPred.pl:370: system("$perlCmdString")==0 or die ("failed to execute: $!\n"); # make augustus.aa
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-371- if ( -f "augustus.aa" ) {# may not exist if nothing was predicted
##############################################
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-385- print "3 mv augustus.gtf ../predictions/\n" if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAugPred.pl:386: system("mv augustus.gtf ../predictions/")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-387- print "3 mv augustus.gff ../predictions/\n" if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAugPred.pl:388: system("mv augustus.gff ../predictions/")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-389-
##############################################
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-397- print "3 $cmdString\n" if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAugPred.pl:398: system("$cmdString")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-399- print "3 mv $gFile ../gbrowse\n" if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAugPred.pl:400: system("mv $gFile ../gbrowse")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-401-
##############################################
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-440- if (! -d $mainDir) {
augustus-3.3.3+dfsg/scripts/autoAugPred.pl:441: system ("mkdir -p $mainDir");
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-442- print "3 Created directory $mainDir.\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-447- for(("gbrowse","shells", "predictions")){mkdir "$_" if (! -d $_);}
augustus-3.3.3+dfsg/scripts/autoAugPred.pl:448: system ("mkdir -p $position/seq/split");
augustus-3.3.3+dfsg/scripts/autoAugPred.pl:449: system ("mkdir -p $position/hints/");
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-450- print "3 All necessary directories have been created under $mainDir\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-470- if(-f "your_job.tmp"){
augustus-3.3.3+dfsg/scripts/autoAugPred.pl:471: system("rm your_job.tmp")==0 or die ("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-472- }
##############################################
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-480- print "3 $cmd\n" if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAugPred.pl:481: system("$cmd")==0 or die ("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-482- $cmd="cat qsub$j.stdout";
augustus-3.3.3+dfsg/scripts/autoAugPred.pl:483: my $output = `$cmd 2>/dev/null`;
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-484- print "3 $output" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-494- print "3 rm your_job.tmp\n" if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAugPred.pl:495: system("rm your_job.tmp")==0 or die ("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-496-}
##############################################
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-509- my $getrunning="ssh $cname \"$clusterENVDefs;${SGEqstatPath}qstat| grep -f $list |wc -l 2>/dev/null\"";
augustus-3.3.3+dfsg/scripts/autoAugPred.pl:510: my $QSTAT_STATUS=`$getrunning`;
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-511- $QSTAT_STATUS=~ s/\n//;
##############################################
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-518- $sleep_now += 30 if ($sleep_now < $sleep_max);
augustus-3.3.3+dfsg/scripts/autoAugPred.pl:519: $QSTAT_STATUS=`$getrunning`;
augustus-3.3.3+dfsg/scripts/autoAugPred.pl-520- $QSTAT_STATUS=~ s/\n//;
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-123-}
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:124:system("mkdir -p $workDir");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-125-
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-175- print "3 $string\n" if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:176: system("ln -s $trainingset training.gb")==0 or die ("failed to execute: $string\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-177- } elsif ($format eq "gff"){ # if it has GFF format, convert it to Genbank format
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-194- print "3 Running \"$cmdString\" ..." if ($verbose >2);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:195: system("$cmdString")==0 or die("failed to execute $!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-196- print " Finished!\n" if ($verbose >2);
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-201- print "3 $perlCmdString\n" if ($verbose>2);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:202: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-203- print "3 training.gb with genbank format has been created under $workDir/seq/training/.\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-222- print "2 Running command \"$perlCmdString\" to create AUGUSTUS config files for new species $species\n" if ($verbose>=2);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:223: system("$perlCmdString")==0 or die("Program aborted $!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-224- open(NSPECIES, "new_species.stdout") or die ("Cannot open new_species.stdout");
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-271- print "2 Creating training.gb.train and training.gb.test with \"$perlCmdString\"...\n" if ($verbose>=2);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:272: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-273- print "2 Created training.gb.train and training.gb.test under $workDir.\n" if ($verbose>=2);
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-293- print "3 $perlCmdString ...\n" if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:294: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:295: system("mv training.gb.train.train training.gb.onlytrain")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-296- print "2 training.gb.train.test and training.gb.onlytrain have been made under $workDir.\n" if ($verbose>=2);
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-315- print "2 First try with etraining: etraining --species=$species training.gb.train >train.out ..." if ($verbose>=2);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:316: system("etraining --species=$species training.gb.train 1>train.out 2>train.err")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-317- print " Finished!\n" if ($verbose>=2);
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-331- chdir "$workDir/training/" or die ("Can not change directory to $workDir/training.");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:332: system("etraining --species=$species training.gb.train 1>train.out 2>train.err")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-333- print " Finished!\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-358- print "2 First evaluation of parameters ...\n2 Executing \"$cmdString\" ..." if ($verbose>=2);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:359: system("$cmdString")==0 or die("failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-360- print " Finished!\n" if ($verbose>=2);
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-378- print "2 Executing \"$cmdString\" ..." if ($verbose>=2);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:379: system("$cmdString")==0 or die("failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-380- print " Finished!\n" if ($verbose>=2);
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-390- print "2 Running $cmdString ..." if ($verbose>1);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:391: system("$cmdString")==0 or die("failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-392- print " Finished!\n" if ($verbose>1);
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-395- print "2 augustus --species=$species training.gb.test > ./test/augustus.2.withoutCRF.out\n" if ($verbose>1);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:396: system("augustus --species=$species training.gb.test > ./test/augustus.2.withoutCRF.out")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-397- }
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-411- print "2 cp $_ $_".'.withoutCRF'."\n" if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:412: system("cp $_ $_".'.withoutCRF')==0 or die("failed to execute: cp $_ $_".'.withoutCRF');
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-413- }
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-422- print "1 Running $cmdString ..." if ($verbose>0);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:423: system("$cmdString")==0 or die("failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-424- print " Finished!\n" if ($verbose>0);
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-427- print "3 augustus --species=$species training.gb.test > ./test/augustus.2.CRF.out\n" if ($verbose>2);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:428: system("augustus --species=$species training.gb.test > ./test/augustus.2.CRF.out")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-429-
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-443- print "2 cp $_ $_".'.CRF'."\n" if ($verbose>1);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:444: system("cp $_ $_".'.CRF')==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-445- }
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-451- print "3 rm $_\n" if ($verbose >= 3);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:452: system("rm $_")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-453- print "3 cp $_".".withoutCRF $_ \n" if ($verbose >= 3);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:454: system("cp $_".".withoutCRF $_")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-455- }
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-498- if (!uptodate(["$positionWD/autoAugPred_hints/predictions/augustus.gtf"],["genemodels.gtf"])){
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:499: system("cp $positionWD/autoAugPred_hints/predictions/augustus.gtf genemodels.gtf");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-500- }
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-520- print "2 Running command: $perlCmdString ..." if ($verbose>=2);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:521: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-522- print " Finished!\n" if ($verbose>=2);
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-530- print "3 Running \"cat utr.gff | perl $string\"..." if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:531: system("cat utr.gff | perl $string > utr.train.gbrowse")==0 or die ("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-532- print " Finished! Made file utr.train.gbrowse\n" if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:533: system("mv utr.train.gbrowse ../../gbrowse")==0 or die ("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-534- print "3 Moved utr.train.gbrowse to $workDir/gbrowse\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-547- close(TRLST);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:548: system("cat tr.lst | sort -u > tr_temp.lst")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:549: system("rm tr.lst")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:550: system("mv tr_temp.lst tr.lst")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-551- open(TR, "tr.lst") or die ("Can not open tr.lst!\n");
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-569- # sort for gff2gbSmallDNA.pl
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:570: system("cat utr.gff genemodels.gtf > genes.gtf_temp")==0 or die ("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-571- open(GENES, "genes.gtf_temp") or die ("Can not open the file genes.gtf_temp");
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-577- close(WRITEGENES);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:578: system("cat genes.gtf_unsort | sort -n -k 4,4 | sort -s -k 10,10 | sort -s -k 1,1 > genes.gtf")==0 or die ("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-579- $string=find("gff2gbSmallDNA.pl");
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-582- print "3 Running \"$perlCmdString\" ..." if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:583: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-584- print " Finished!\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-610- $count=0;
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:611: system("cp ../training.gb.train.test t.gb")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-612- open(TEMP2,"t.gb") or die {"Can not open the file t.gb! \n"};
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-623- print "3 Running \"$perlCmdString\"..." if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:624: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-625- print " Finished!\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-627- print "3 Running \"$perlCmdString\"..." if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:628: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-629- print " Finished!\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-639- close(NOMRNA);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:640: system("cat t.nomrna.test.gb bothutr.test.gb.test > train.gb")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-641-
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-649- print "1 Have constructed a training set train.gb for UTRs with $counter_gen genes\n" if ($verbose>=1);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:650: system("rm t.gb.train t.gb t.gb.test t.nomrna.test.gb")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:651:# system('grep LOCUS train.gb | perl -pe \'s/^LOCUS\s+(\S+)\s+.*/$1/\' > train.gb.lst')==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-652-# print "3 Made file train.gb.lst under $workDir/training/utr/\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-658-
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:659: system("cp ../training.gb.onlytrain ./")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-660- open(ONLYTRAIN, "training.gb.onlytrain") or die ("Can not open training.gb.onlytrain.");
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-671- close(CDSONLY);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:672: system("rm training.gb.onlytrain")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-673-
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-688- $perlCmdString="perl $string remove.lst bothutr.test.gb > train.utronly.gb";
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:689: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:690: system("cat cdsonly.gb train.utronly.gb > onlytrain.gb")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-691- print "2 Made onlytrain.gb under $workDir/training/utr/\n" if ($verbose>=2);
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-704- close(PARATEMP);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:705: system("rm $paraName")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:706: system("mv cfg_temp $paraName")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-707- chdir "$workDir/training/utr" or die ("Error: could not chdir to $workDir/training/utr!\n");
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-718- print "1 Running \"$perlCmdString\"..." if ($verbose>=1);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:719: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-720- print " finished" if ($verbose>=3);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:721: system("cat train.gb ../training.gb.train > train.all.gb")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-722- } else {
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-727- print "\n2 Running $perlCmdString ..." if ($verbose>=2);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:728: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-729- if ($CRFtrain){
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-730- # TODO: check what is better at the end
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:731: system("etraining --species=$species --UTR=on train.all.gb --CRF=1 1>etrain.out 2>etrain.err")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-732- }
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-833- print "3 $cmdString ..." if ($verbose>2);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:834: system("$cmdString")==0 or die("Program aborted. Possibly \"scipio\" is not installed or not in your PATH");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-835- print "Finished.\n" if ($verbose>2);
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-837- print "3 $cmdString ..." if ($verbose>2);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:838: system("$cmdString")==0 or die("Command aborted. Possibly \"scipio\" is not installed or not in your PATH\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-839- print "Finished.\n" if ($verbose>2);
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-842- print "3 $cmdString ..." if ($verbose>2);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:843: system("$cmdString")==0 or die("Command aborted.\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-844- print "Finished.\n" if ($verbose>2);
##############################################
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-856- print "3 $perlCmdString\n" if ($verbose>2);
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl:857: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/scripts/autoAugTrain.pl-858- print "3 training.gb with genbank format has been created under $workDir/seq/training/.\n" if ($verbose>2);
##############################################
augustus-3.3.3+dfsg/scripts/checkParamArchive.pl-18-# extract archive
augustus-3.3.3+dfsg/scripts/checkParamArchive.pl:19:`cd $projectDir; tar xzvf $parArch`;
augustus-3.3.3+dfsg/scripts/checkParamArchive.pl:20:my $speciesName = `ls $projectDir`;
augustus-3.3.3+dfsg/scripts/checkParamArchive.pl-21-chomp($speciesName);
##############################################
augustus-3.3.3+dfsg/scripts/createAugustusJoblist.pl-178- close JOB;
augustus-3.3.3+dfsg/scripts/createAugustusJoblist.pl:179: system("chmod +x $jobname");
augustus-3.3.3+dfsg/scripts/createAugustusJoblist.pl-180- }
##############################################
augustus-3.3.3+dfsg/scripts/evalCGP.pl-168-my $gffDir = "tempGFF";
augustus-3.3.3+dfsg/scripts/evalCGP.pl:169:system ("rm -rf $gffDir; mkdir $gffDir");
augustus-3.3.3+dfsg/scripts/evalCGP.pl-170-
##############################################
augustus-3.3.3+dfsg/scripts/evalCGP.pl-240-if($joingenes){
augustus-3.3.3+dfsg/scripts/evalCGP.pl:241: system("mv $gffDir/pred.gtf $gffDir/pred.unfiltered.gtf");
augustus-3.3.3+dfsg/scripts/evalCGP.pl:242: system("$cmdpars{'jg_exec_dir'}joingenes $jg_pars -g $gffDir/pred.unfiltered.gtf -o $gffDir/pred.gtf");
augustus-3.3.3+dfsg/scripts/evalCGP.pl-243-}
##############################################
augustus-3.3.3+dfsg/scripts/evalCGP.pl-246-# list files that contain the directories of the GTF files being compared (required by eval)
augustus-3.3.3+dfsg/scripts/evalCGP.pl:247:system ("rm -f $gffDir/annotation_list");
augustus-3.3.3+dfsg/scripts/evalCGP.pl:248:system ("rm -f $gffDir/prediction_list");
augustus-3.3.3+dfsg/scripts/evalCGP.pl-249-foreach my $seq (keys %seqlist) {
augustus-3.3.3+dfsg/scripts/evalCGP.pl:250: system ("echo '$gffDir/$seq.anno.gtf' >> $gffDir/annotation_list");
augustus-3.3.3+dfsg/scripts/evalCGP.pl:251: system ("echo '$gffDir/$seq.pred.gtf' >> $gffDir/prediction_list");
augustus-3.3.3+dfsg/scripts/evalCGP.pl:252: system ("grep \"^$seq\\b\" $gffDir/pred.gtf > $gffDir/$seq.pred.gtf");
augustus-3.3.3+dfsg/scripts/evalCGP.pl:253: system ("grep \"^$seq\\b\" $gffDir/anno.gtf > $gffDir/$seq.anno.gtf");
augustus-3.3.3+dfsg/scripts/evalCGP.pl-254-}
##############################################
augustus-3.3.3+dfsg/scripts/evalCGP.pl-256-# call evaluate_gtf
augustus-3.3.3+dfsg/scripts/evalCGP.pl:257:system ("$cmdpars{'eval_exec_dir'}evaluate_gtf.pl $gffDir/annotation_list $gffDir/prediction_list");
##############################################
augustus-3.3.3+dfsg/scripts/eval_dualdecomp.pl-82-if ($outdir ne ""){
augustus-3.3.3+dfsg/scripts/eval_dualdecomp.pl:83: system ("rm -rf $outdir; mkdir $outdir");
augustus-3.3.3+dfsg/scripts/eval_dualdecomp.pl-84- $outdir =~ s/([^\/])$/$1\//g;
##############################################
augustus-3.3.3+dfsg/scripts/eval_multi_gtf.pl-70-my $dirname = "tempgtf";
augustus-3.3.3+dfsg/scripts/eval_multi_gtf.pl:71:system("rm -rf $dirname; mkdir $dirname");
augustus-3.3.3+dfsg/scripts/eval_multi_gtf.pl-72-
##############################################
augustus-3.3.3+dfsg/scripts/eval_multi_gtf.pl-85- . "_plus.anno.gtf";
augustus-3.3.3+dfsg/scripts/eval_multi_gtf.pl:86: system($cmdStr);
augustus-3.3.3+dfsg/scripts/eval_multi_gtf.pl-87- $cmdStr = "grep \"^$seq\\b\" $predfilename | grep -P \"\\t\\+\\t\" > "
##############################################
augustus-3.3.3+dfsg/scripts/eval_multi_gtf.pl-89- . "_plus.pred.gtf";
augustus-3.3.3+dfsg/scripts/eval_multi_gtf.pl:90: system($cmdStr);
augustus-3.3.3+dfsg/scripts/eval_multi_gtf.pl:91: system( "echo '$dirname/$seq" . "_plus.anno.gtf' >> annotation_list" );
augustus-3.3.3+dfsg/scripts/eval_multi_gtf.pl:92: system( "echo '$dirname/$seq" . "_plus.pred.gtf' >> prediction_list" );
augustus-3.3.3+dfsg/scripts/eval_multi_gtf.pl-93- system( "grep \"^$seq\\b\" $annofilename | grep -P \"\\t-\\t\" > "
##############################################
augustus-3.3.3+dfsg/scripts/eval_multi_gtf.pl-98- . "_minus.pred.gtf" );
augustus-3.3.3+dfsg/scripts/eval_multi_gtf.pl:99: system( "echo '$dirname/$seq" . "_minus.anno.gtf' >> annotation_list" );
augustus-3.3.3+dfsg/scripts/eval_multi_gtf.pl:100: system( "echo '$dirname/$seq" . "_minus.pred.gtf' >> prediction_list" );
augustus-3.3.3+dfsg/scripts/eval_multi_gtf.pl-101-
##############################################
augustus-3.3.3+dfsg/scripts/eval_multi_gtf.pl-105-#
augustus-3.3.3+dfsg/scripts/eval_multi_gtf.pl:106:system( "perl -I $evalpath $evalpath/evaluate_gtf.pl annotation_list prediction_list 2> /dev/null" );
augustus-3.3.3+dfsg/scripts/eval_multi_gtf.pl-107-
##############################################
augustus-3.3.3+dfsg/scripts/filterGenesOut_mRNAname.pl-73-#checks whether a gene name exists in reference file
augustus-3.3.3+dfsg/scripts/filterGenesOut_mRNAname.pl:74:@line = `grep $genename $goodfilename`;
augustus-3.3.3+dfsg/scripts/filterGenesOut_mRNAname.pl-75-if(length($line[0])<1){
##############################################
augustus-3.3.3+dfsg/scripts/gbrowseold2gff3.pl-16-
augustus-3.3.3+dfsg/scripts/gbrowseold2gff3.pl:17:exec("perldoc $0") if ($help);
augustus-3.3.3+dfsg/scripts/gbrowseold2gff3.pl-18-
##############################################
augustus-3.3.3+dfsg/scripts/gtf2bed.pl-20-
augustus-3.3.3+dfsg/scripts/gtf2bed.pl:21:exec("perldoc $0") if ($help);
augustus-3.3.3+dfsg/scripts/gtf2bed.pl-22-
##############################################
augustus-3.3.3+dfsg/scripts/gtf2gff.pl-35-
augustus-3.3.3+dfsg/scripts/gtf2gff.pl:36:exec("perldoc $0") if ($help || !defined($outfile));
augustus-3.3.3+dfsg/scripts/gtf2gff.pl-37-
##############################################
augustus-3.3.3+dfsg/scripts/maf2conswig.pl-32-
augustus-3.3.3+dfsg/scripts/maf2conswig.pl:33:exec("perldoc $0") if ($help);
augustus-3.3.3+dfsg/scripts/maf2conswig.pl-34-
##############################################
augustus-3.3.3+dfsg/scripts/new_species.pl-148- }
augustus-3.3.3+dfsg/scripts/new_species.pl:149: system ("cp $configdir/species/generic/generic_weightmatrix.txt $weightfilename");
augustus-3.3.3+dfsg/scripts/new_species.pl-150-}else{
##############################################
augustus-3.3.3+dfsg/scripts/new_species.pl-153- }
augustus-3.3.3+dfsg/scripts/new_species.pl:154: system ("cp $configdir/species/template_prokaryotic/template_prokaryotic_weightmatrix.txt $weightfilename");
augustus-3.3.3+dfsg/scripts/new_species.pl-155-}
##############################################
augustus-3.3.3+dfsg/scripts/new_species.pl-162- }
augustus-3.3.3+dfsg/scripts/new_species.pl:163: system ("cp $configdir/species/generic/generic_metapars.cfg $metafilename");
augustus-3.3.3+dfsg/scripts/new_species.pl:164: system ("cp $configdir/species/generic/generic_metapars.utr.cfg $metautrfilename");
augustus-3.3.3+dfsg/scripts/new_species.pl:165: system ("cp $configdir/species/generic/generic_metapars.cgp.cfg $metacgpfilename");
augustus-3.3.3+dfsg/scripts/new_species.pl-166-}else{
##############################################
augustus-3.3.3+dfsg/scripts/new_species.pl-169- }
augustus-3.3.3+dfsg/scripts/new_species.pl:170: system ("cp $configdir/species/template_prokaryotic/template_prokaryotic_metapars.cfg $metafilename");
augustus-3.3.3+dfsg/scripts/new_species.pl:171: system ("cp $configdir/species/template_prokaryotic/template_prokaryotic_metapars.utr.cfg $metautrfilename");
augustus-3.3.3+dfsg/scripts/new_species.pl-172-}
##############################################
augustus-3.3.3+dfsg/scripts/new_species.pl-179- }
augustus-3.3.3+dfsg/scripts/new_species.pl:180: system ("cp $configdir/species/template_prokaryotic/template_prokaryotic_ovlp_len.pbl $ovlpfilename");
augustus-3.3.3+dfsg/scripts/new_species.pl-181- print "creating $transshadowfilename ..\n";
##############################################
augustus-3.3.3+dfsg/scripts/new_species.pl-184- }
augustus-3.3.3+dfsg/scripts/new_species.pl:185: system ("cp $configdir/species/template_prokaryotic/template_prokaryotic_trans_shadow_bacterium.pbl $transshadowfilename");
augustus-3.3.3+dfsg/scripts/new_species.pl-186-}
##############################################
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-393-my $optdir = "tmp_opt_$cmdpars{'species'}";
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl:394:system("rm -rf $optdir;mkdir $optdir");
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-395-opendir( TMPDIR, $optdir ) or die("Could not open $optdir");
##############################################
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-475- # make the temporary training and testing files
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl:476: system("rm -f $optdir/curtrain-$k");
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-477- for ( my $m = 1; $m <= $cmdpars{"kfold"}; $m++ ) {
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-478- if ( $m != $k ) {
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl:479: system("cat $optdir/bucket$m.gb >> $optdir/curtrain-$k");
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-480- }
##############################################
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-482- if ( $cmdpars{'onlytrain'} ne '' ) {
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl:483: system("cat $cmdpars{'onlytrain'} >> $optdir/curtrain-$k");
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-484- }
##############################################
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-660- close(ORIG);
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl:661: system("cp $species_cfg_filename $species_cfg_filename.orig$y");
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-662- }
##############################################
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-996- # delete the temporary training files
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl:997: system("rm -f $optdir/curtrain-$k $optdir/predictions-$k.txt");
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-998- }
##############################################
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-1002- # make the joint training file (train.gb and onlytrain.gb)
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl:1003: system("rm -f $optdir/curtrain $optdir/curtest");
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl:1004: system("cp $cmdpars{'train.gb'} $optdir/curtrain");
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-1005- if ( $cmdpars{'onlytrain'} ne '' ) {
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl:1006: system("cat $cmdpars{'onlytrain'} >> $optdir/curtrain");
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-1007- }
##############################################
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-1014- print "$cmd\n";
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl:1015: system($cmd);
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl:1016: system("rm -f $optdir/curtrain");
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-1017-}
##############################################
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-1023-if($cmdpars{'cleanup'}==1){
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl:1024: system ("rm -rf $optdir");
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-1025-}
##############################################
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-1072- # make the temporary training and testing files
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl:1073: system("rm -f $optdir/curtrain $optdir/curtest");
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl:1074: system("cp $optdir/bucket$k.gb $optdir/curtest");
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-1075- for ( my $m = 1; $m <= $cmdpars{"kfold"}; $m++ ) {
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-1076- if ( $m != $k ) {
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl:1077: system("cat $optdir/bucket$m.gb >> $optdir/curtrain");
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-1078- }
##############################################
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-1080- if ( $cmdpars{'onlytrain'} ne '' ) {
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl:1081: system("cat $cmdpars{'onlytrain'} >> $optdir/curtrain");
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-1082- }
##############################################
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-1090- .= "$cmdpars{'aug_exec_dir'}etraining --species=$cmdpars{'species'} --AUGUSTUS_CONFIG_PATH=$configdir $argument $pars $be_silent $modelrestrict $optdir/curtrain";
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl:1091: system($cmd);
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-1092- }
##############################################
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-1098- .= "$cmdpars{'aug_exec_dir'}augustus --species=$cmdpars{'species'} --AUGUSTUS_CONFIG_PATH=$configdir $argument $pars $optdir/curtest > $optdir/predictions.txt";
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl:1099: system($cmd);
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-1100-
##############################################
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-1173- . "$be_silent $modelrestrict $pbloutfiles $optdir/curtrain-$k";
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl:1174: system($cmd);
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-1175-
##############################################
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-1187- .= "$cmdpars{'aug_exec_dir'}augustus --species=$cmdpars{'species'} --AUGUSTUS_CONFIG_PATH=$configdir $argument $pars $pblinfiles $optdir/bucket$k.gb > $optdir/predictions-$k.txt";
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl:1188: system($cmd);
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-1189- print "$k ";
##############################################
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-1259- # this part is done in parallel by the child process
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl:1260: system("rm -rf $optdir/pred$k; mkdir $optdir/pred$k");
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-1261- my $cmd = "";
##############################################
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-1266- .= "$cmdpars{'aug_exec_dir'}augustus --species=$cmdpars{'species'} --AUGUSTUS_CONFIG_PATH=$configdir $argument $pars --alnfile=$optdir/splitMaf/$k.maf --/CompPred/outdir=$optdir/pred$k >$optdir/pred$k/aug.out";
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl:1267: system($cmd);
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-1268- print "$k ";
##############################################
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-2042- my $mafDir = "$optdir/splitMaf";
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl:2043: system("rm -rf $mafDir; mkdir $mafDir");
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-2044-
##############################################
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-2052- { # in the serial case just make a temporary copy of the whole alignment
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl:2053: system("cp $cmdpars{'alnfile'} $mafDir/$cmdpars{'kfold'}.maf");
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-2054- }
##############################################
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-2122- my $gffDir = "$optdir/tempGFF";
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl:2123: system("rm -rf $gffDir; mkdir $gffDir");
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-2124-
##############################################
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-2205- if ($joingenes) {
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl:2206: system("mv $optdir/pred.gtf $optdir/pred.unfiltered.gtf");
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-2207- my $cmd = "";
##############################################
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-2212- .= "$cmdpars{'jg_exec_dir'}joingenes -g $optdir/pred.unfiltered.gtf -o $optdir/pred.gtf";
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl:2213: system($cmd);
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-2214- }
##############################################
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-2217-# list files that contain the directories of the GTF files being compared (required by eval)
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl:2218: system("rm -f $optdir/annotation_list");
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl:2219: system("rm -f $optdir/prediction_list");
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-2220- foreach my $seq ( keys %seqlist ) {
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl:2221: system("echo '$gffDir/$seq.anno.gtf' >> $optdir/annotation_list");
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl:2222: system("echo '$gffDir/$seq.pred.gtf' >> $optdir/prediction_list");
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl:2223: system("grep \"^$seq\\b\" $optdir/pred.gtf > $gffDir/$seq.pred.gtf");
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl:2224: system("grep \"^$seq\\b\" $optdir/anno.gtf > $gffDir/$seq.anno.gtf");
augustus-3.3.3+dfsg/scripts/optimize_augustus.pl-2225- }
##############################################
augustus-3.3.3+dfsg/scripts/parseSim4Output.pl-116- # let cdbyank use the index to search the sequence
augustus-3.3.3+dfsg/scripts/parseSim4Output.pl:117: system("echo '$seqname' | cdbyank ${seqfilename}.cidx -d $seqfilename > genomic.fa");
augustus-3.3.3+dfsg/scripts/parseSim4Output.pl-118- system ("perl -i.orig -p -e 's/^Incorrectly.*fixed.\n//' genomic.fa");
##############################################
augustus-3.3.3+dfsg/scripts/peptides2alternatives.pl-88- ## map pulled transcripts
augustus-3.3.3+dfsg/scripts/peptides2alternatives.pl:89: `$blat -t=prot -q=prot -noHead $target $toBeMapped $tmpPsl`;
augustus-3.3.3+dfsg/scripts/peptides2alternatives.pl-90- ## read in psl file, delete already mapped peptides, print psl
##############################################
augustus-3.3.3+dfsg/scripts/peptides2alternatives.pl-97- close(PSL) or die "Could not close psl file $tmpPsl!\n";
augustus-3.3.3+dfsg/scripts/peptides2alternatives.pl:98: `rm $toBeMapped`;
augustus-3.3.3+dfsg/scripts/peptides2alternatives.pl-99-}
augustus-3.3.3+dfsg/scripts/peptides2alternatives.pl-100-print STDERR "Done!\n";
augustus-3.3.3+dfsg/scripts/peptides2alternatives.pl:101:`rm $target $tmpPsl`;
##############################################
augustus-3.3.3+dfsg/scripts/pslMap.pl-40-
augustus-3.3.3+dfsg/scripts/pslMap.pl:41:exec("perldoc $0") if ($help || !defined($infile) || !defined($outfile) || !(defined($mapfile)));
augustus-3.3.3+dfsg/scripts/pslMap.pl-42-
##############################################
augustus-3.3.3+dfsg/scripts/runAllSim4.pl-12- $estfilename = shift @f;
augustus-3.3.3+dfsg/scripts/runAllSim4.pl:13: system ("echo '$estfilename' | cdbyank ~/galdieria/galdi3/Newbler_all_454AllContigs.fna.long.uc.cidx > mrna.fa");
augustus-3.3.3+dfsg/scripts/runAllSim4.pl-14- system ("echo '@f' | cdbyank ~/galdieria/galdi3/build3.fa.cidx > genomic.fa");
##############################################
augustus-3.3.3+dfsg/scripts/runAllSim4.pl-18- close LONG;
augustus-3.3.3+dfsg/scripts/runAllSim4.pl:19: system ("echo '--------\n>$estfilename' >> sim4.results");
augustus-3.3.3+dfsg/scripts/runAllSim4.pl-20- system ("sim4 mrna.fa genomic.fa.long >> sim4.results");
##############################################
augustus-3.3.3+dfsg/scripts/weedMaf.pl-24-
augustus-3.3.3+dfsg/scripts/weedMaf.pl:25:exec("perldoc $0") if ($help);
augustus-3.3.3+dfsg/scripts/weedMaf.pl-26-
##############################################
augustus-3.3.3+dfsg/scripts/wig2hints.pl-14-if( grep /^--?h$/, @ARGV ) {
augustus-3.3.3+dfsg/scripts/wig2hints.pl:15: exec("perldoc $0");
augustus-3.3.3+dfsg/scripts/wig2hints.pl-16-}
##############################################
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-40- ## create the webserver output directory
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl:41: `mkdir $projectWebOutDir`;
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-42- if (not(-d "$projectWebOutDir")){
##############################################
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-55- $cmdStr = "cat $head $segmentFile2 $tail > $projectWebOutDir/index.html";
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl:56: `$cmdStr`;
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-57- unlink $segmentFile2;
##############################################
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-64- my $projectWebOutParams = $wwwOut."/$projectID/$species";
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl:65: `mkdir $projectWebOutParams`;
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-66- if (not(-d "$projectWebOutParams")){
##############################################
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-155- $cmdStr = "cd $projectWebOutDir; tar -czvf parameters.tar.gz $species &> /dev/null;";
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl:156: `$cmdStr`;
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-157- }
##############################################
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-176- if(-d $cfgFilesDir){
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl:177: `rm -r $cfgFilesDir`;
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-178- print STDERR "Deleting $cfgFilesDir because no relevant parameters can have been produced.\n";4
##############################################
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-181- $cmdStr = "cp $trainingFile $projectWebOutDir/training.gb; cd $projectWebOutDir; gzip training.gb &> /dev/null;";
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl:182: `$cmdStr`;
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-183- }
##############################################
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-200- $cmdStr = "cp $ab_initio_grailsDir/predictions/* $ab_initio_webDir; cp $ab_initio_grailsDir/gbrowse/* $ab_initio_webDir;";
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl:201: `$cmdStr`;
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-202- $cmdStr = "cd $projectWebOutDir; tar -czvf ab_initio.tar.gz ab_initio;";
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl:203: `$cmdStr`;
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-204- $cmdStr = "rm -r $ab_initio_webDir;";
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl:205: `$cmdStr`;
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-206- }
##############################################
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-221- $cmdStr = "cp $hintsPred_grailsDir/predictions/* $hintsPred_webDir; cp $hintsPred_grailsDir/gbrowse/* $hintsPred_webDir;";
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl:222: `$cmdStr`;
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-223- $cmdStr = "cd $projectWebOutDir; tar -czvf hints_pred.tar.gz hints_pred;";
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl:224: `$cmdStr`;
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-225- $cmdStr = "rm -r $hintsPred_webDir;";
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl:226: `$cmdStr`;
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-227- }
##############################################
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-240- $cmdStr = "cp $utrPred_grailsDir/predictions/* $utrPred_webDir; cp $utrPred_grailsDir/gbrowse/* $utrPred_webDir;";
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl:241: `$cmdStr`;
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-242- $cmdStr = "cd $projectWebOutDir; tar -czvf utr_pred.tar.gz utr_pred;";
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl:243: `$cmdStr`;
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-244- $cmdStr = "rm -r $utrPred_webDir;";
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl:245: `$cmdStr`;
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-246- }
##############################################
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-260- $cmdStr = "cp $utrHintsPred_grailsDir/predictions/* $utrHintsPred_webDir; cp $utrHintsPred_grailsDir/gbrowse/* $utrHintsPred_webDir;";
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl:261: `$cmdStr`;
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-262- $cmdStr = "cd $projectWebOutDir; tar -czvf hints_utr_pred.tar.gz hints_utr_pred;";
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl:263: `$cmdStr`;
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-264- $cmdStr = "rm -r $utrHintsPred_webDir;";
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl:265: `$cmdStr`;
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-266- }
##############################################
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-273- $cmdStr = "cp $errorFile $projectWebOutDir; cp $logFile $projectWebOutDir;";
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl:274: `$cmdStr`;
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-275- }else{
##############################################
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-284- $cmdStr = "cd $grailsOut/$projectID; tar -czvf predictions.tar.gz augustus;";
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl:285: `$cmdStr`;
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-286- $cmdStr = "cp $grailsOut/$projectID/predictions.tar.gz $projectWebOutDir/predictions.tar.gz";
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl:287: `$cmdStr`;
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-288- }
##############################################
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-350-$cmdStr = "cat $head $segmentFile2 $tail > $projectWebOutDir/index.html";
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl:351:`$cmdStr`;
augustus-3.3.3+dfsg/scripts/writeResultsPage.pl-352-unlink $segmentFile2;
##############################################
augustus-3.3.3+dfsg/src/googletest/src/gtest.cc-3168- } else {
augustus-3.3.3+dfsg/src/googletest/src/gtest.cc:3169: printf(", where %s = %s\n", kTypeParamLabel, test_suite.type_param());
augustus-3.3.3+dfsg/src/googletest/src/gtest.cc-3170- }
##############################################
augustus-3.3.3+dfsg/src/googletest/src/gtest.cc-5487- // the output easy to parse by a program.
augustus-3.3.3+dfsg/src/googletest/src/gtest.cc:5488: PrintOnOneLine(test_suite->type_param(), kMaxParamLength);
augustus-3.3.3+dfsg/src/googletest/src/gtest.cc-5489- }
##############################################
augustus-3.3.3+dfsg/src/googletest/src/gtest.cc-5496- // output easy to parse by a program.
augustus-3.3.3+dfsg/src/googletest/src/gtest.cc:5497: PrintOnOneLine(test_info->value_param(), kMaxParamLength);
augustus-3.3.3+dfsg/src/googletest/src/gtest.cc-5498- }
##############################################
augustus-3.3.3+dfsg/src/randseqaccess.cc-762- Statement stmt(&db);
augustus-3.3.3+dfsg/src/randseqaccess.cc:763: stmt.prepare("SELECT start,end, offset, streamsize FROM genomes as G,speciesnames as S,seqnames as N WHERE speciesname=$1 AND seqname=$2 \
augustus-3.3.3+dfsg/src/randseqaccess.cc-764- AND G.speciesid=S.speciesid AND S.speciesid=N.speciesid AND G.seqnr=N.seqnr AND start <=?3 AND end >=?4 ORDER BY start ASC;");
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/aa2nonred.pl-179- if($CPU > 1){
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/aa2nonred.pl:180: system("$DIAMOND_PATH/diamond makedb --in $tempdbname -d $tempdbname --threads $CPU");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/aa2nonred.pl-181- }else{
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/aa2nonred.pl:182: system("$DIAMOND_PATH/diamond makedb --in $tempdbname -d $tempdbname --threads 1");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/aa2nonred.pl-183- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/aa2nonred.pl-185- ## NCBI blast
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/aa2nonred.pl:186: system("$BLAST_PATH/makeblastdb -in $tempdbname -dbtype prot -parse_seqids -out $tempdbname");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/aa2nonred.pl-187-}
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/aa2nonred.pl-190- if($diamond){
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/aa2nonred.pl:191: system("$DIAMOND_PATH/diamond blastp --db $tempdbname --outfmt 0 --query $tempdbname --out $tempoutfile")
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/aa2nonred.pl-192-
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/aa2nonred.pl-193- }else{
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/aa2nonred.pl:194: system("$BLAST_PATH/blastp -query $tempdbname -db $tempdbname > $tempoutfile");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/aa2nonred.pl-195- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/aa2nonred.pl-197- if($diamond){
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/aa2nonred.pl:198: system("$DIAMOND_PATH/diamond blastp --db $tempdbname --outfmt 0 --query $tempdbname --threads $CPU --out $tempoutfile");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/aa2nonred.pl-199- }else{
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/aa2nonred.pl-202- my $pid = $pm->start and next;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/aa2nonred.pl:203: system("$BLAST_PATH/blastp -query $tempdbname -db $tempdbname > $_.blastout");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/aa2nonred.pl-204- $pm->finish;
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/aa2nonred.pl-207- foreach ( @splitFiles ) {
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/aa2nonred.pl:208: system("cat $_.blastout >> $tempoutfile");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/aa2nonred.pl-209- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-212- print "3 $perlCmdString\n" if ($verbose>2);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:213: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-214- unless(-e $genome_clean){die("Clean genome file $genome_clean does not exist!\n");}
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-319- print "3 ln -s $genome genome.fa\n" if($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:320: system("ln -s $genome genome.fa")==0 or die("\nfailed to execute ln -s $genome genome.fa\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-321- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-365- print "3 ln -fs $fasta_cdna transcripts.fasta\n" if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:366: system("ln -fs $fasta_cdna transcripts.fasta")==0 or die ("failed to execute: ln -fs $fasta_cdna transcripts.fasta\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-367- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-372- print "2 Running $perlCmdString ..." if ($verbose>=2);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:373: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-374- print " Finished!\n" if ($verbose>=2);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-385- print "3 $cmdString\n" if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:386: system("$cmdString")==0 or die ("failed to execute: $cmdString\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-387-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-404- print "3 $cmdString\n" if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:405: system("$cmdString")==0 or die ("failed to execute: $cmdString\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-406- print "3 Adjusted alignAssembly.config\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-416- print "3 $cmdString\n" if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:417: system("$cmdString")==0 or die("\nfailed to execute $cmdString\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-418-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-462-
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:463: system("$perlCmdString")==0 or die ("$abortString");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-464- print " Finished\n" if ($verbose>=2);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-473- print "2 Running $perlCmdString ..." if ($verbose>=2);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:474: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-475- print " Finished\n" if ($verbose>=2);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-487- print "3 Deleting $file\n" if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:488: system("$perlCmdString");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-489- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-501- print "3 $cmdString 1> pasa.complete.lst\n" if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:502: system("$cmdString 1> pasa.complete.lst")==0 or die("\nfailed to execute $cmdString\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-503- if (! -e "pasa.complete.lst" || -z "pasa.complete.lst"){
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-507- print "2 Running \"$cmdString\" ..." if ($verbose>=2);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:508: system("$cmdString")==0 or die("\nfailed to execute $cmdString\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-509- print " Finished!\n" if ($verbose>=2);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-516- print "2 Running \"$cmdString\" ..." if ($verbose >=2);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:517: system("$cmdString")==0 or die("\nfailed to execute $cmdString\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-518- print " Finished!\n" if ($verbose >=2);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-552- print "3 $perlCmdString\n" if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:553: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-554-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-569- print "3 $cmdString\n" if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:570: system("$cmdString")==0 or die ("failed to execute: $cmdString\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-571-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-576- print "3 $cmdString\n" if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:577: system("$cmdString")==0 or die ("failed to execute: $cmdString\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-578-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-583- # $cmdString="mv $trainDir/pasa/trainingSetComplete.gb $trainDir/training/trainingSetComplete.gb";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:584: # system("$cmdString")==0 or die("\nfailed to move trainingSetComplete.gb to $trainDir/training\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-585- print "3 cd $trainDir/training\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-588- print "3 Running \"$cmdString\" ... " if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:589: system("$cmdString")==0 or die("\nfailed to execute: $cmdString\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-590- print " Finished!\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-599- chdir "$genericPathTrain" or die ("Can not chdir to $genericPathTrain.\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:600: system('cat generic_parameters.cfg | perl -pe \'s/(stopCodonExcludedFromCDS ).*/$1false /\' > '."${species}_generic_parameters.cfg")==0 or die ("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-601- print "3 Set value of \"stopCodonExcludedFromCDS\" in ${species}_generic_parameters.cfg to \"false\"\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-605- print "3 Running \"$cmdString\" ... " if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:606: system("$cmdString")==0 or die("\nfailed to execute: $cmdString\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-607- print " Finished!\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-616- print "3 $cmdString\n" if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:617: system("$cmdString")==0 or die ("failed to execute: $cmdString\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-618-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-623- print "3 Running $perlCmdString ...\n" if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:624: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-625-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-639- print "3 Running $perlCmdString ..." if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:640: system("$perlCmdString")==0 or die("\nfailed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-641- print " Finished!\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-654- print "3 Running $perlCmdString ..." if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:655: system("$perlCmdString")==0 or die("\nfailed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-656- print " Finished!\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-660- print "3 Running $cmdString ..." if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:661: system("$cmdString")==0 or die("\nfailed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-662- print " Finished!\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-671- if (!uptodate([$fasta_cdna], ["cdna.fa"])){
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:672: system("ln -fs $fasta_cdna cdna.fa")==0 or die ("failed to execute: ln -fs $fasta_cdna cdna.fa");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-673- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-682-
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:683: system("$cmdString")==0 or die("$abortString");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-684- print "Finished!\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-701-
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:702: if (system("$cmdString") != 0) {
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-703- print "WARNING: Could not successfully find and run pslCDnaFilter. Please install this program.\n";
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-711- print "3 Running $perlCmdString ..." if ($verbose>3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:712: system("$perlCmdString")==0 or die("\nFailed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-713- print " Finished!\n" if ($verbose>3);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-720- print "2 Running $perlCmdString ..." if ($verbose>=2);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:721: system("$perlCmdString")==0 or die("\nfailed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-722- print " Finished!\n" if ($verbose>=2);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-731- print "2 Running $perlCmdString ..." if ($verbose>=2);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:732: system("$perlCmdString")==0 or die("\nfailed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-733- print " Finished!\n" if ($verbose>=2);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-738- print "3 Running $perlCmdString.\n" if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:739: system("$perlCmdString")==0 or die("\nfailed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-740- rename("../hints/hints.E.gff.temp","../hints/hints.E.gff");
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-761- print "\n2 $perlCmdString\n" if ($verbose>=2);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:762: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-763-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-800- print "2 $perlCmdString\n" if ($verbose>=2);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:801: system("$perlCmdString")==0 or die("\nfailed to execute $perlCmdString\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-802-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-862- chdir $positionWD;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:863: system("$perlCmdString")==0 or die ("$abortString");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-864-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-901- print "2 $perlCmdString ...\n" if ($verbose>1);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:902: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-903-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-932- print "\n2 $perlCmdString\n" if ($verbose>=2);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:933: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-934-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-956- }
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:957: system("mkdir -p $summary_dir")==0 or die("\nCould not create directory $summary_dir.\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-958-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-967- chdir "gbrowse";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:968: system ("ln -sf $genome genome.fa") if (!uptodate([$genome], ["genome.fa"]));
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-969-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-971- $cmdString = "cp $rootDir/seq/contigs.gff contigs.gff";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:972: system("$cmdString")==0 or die("\nfailed to execute: $cmdString\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-973-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-975- $cmdString = "ln -sf $rootDir/cdna/cdna.gbrowse cdna.gbrowse";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:976: system("$cmdString")==0 or die("\nfailed to execute: $cmdString\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-977- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-980- $cmdString = "ln -sf $fasta_cdna cdna.fa";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:981: system("$cmdString")==0 or die("\nfailed to execute: $cmdString\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-982- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-991- print "3 $cmdString\n" if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:992: system("$cmdString")==0 or die ("Could not execute $cmdString");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-993- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-1000- $cmdString="ln -sf $rootDir/hints/hints.E.gff hints.E.gff";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:1001: system("$cmdString")==0 or die("\nfailed to execute: $cmdString\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-1002- print "3 $cmdString\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-1004- $cmdString="ln -sf $hints hints.E.gff";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:1005: system("$cmdString")==0 or die("\nfailed to execute: $cmdString\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-1006- print "3 $cmdString\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-1021- print "3 $cmdString\n" if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:1022: system("$cmdString")==0 or die ("Could not execute $cmdString");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-1023- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-1029-
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:1030: system("$cmdString")==0 or die("\nfailed to execute: $cmdString\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-1031- print "3 $cmdString\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-1039- print "3 $cmdString\n" if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:1040: system("$cmdString")==0 or die ("failed to execute: $cmdString\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-1041- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-1048- "find $rootDir/autoAugTrain -name \"*.gb.*\" | grep -v .gb.lst >> tempgbn")){
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:1049: system("$_")==0 or die("\nfailed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-1050- print "3 $_\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-1057- $cmdString="ln -fs $1$2 $2"."_another";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:1058: system("$cmdString")==0 or die("\nfailed to execute: $cmdString\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-1059- print "3 $cmdString\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-1062- $cmdString="ln -s $1$2 $2";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:1063: system("$cmdString")==0 or die("\nfailed to execute: $cmdString\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-1064- print "3 $cmdString\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-1067- print "3 rm tempgbn\n" if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl:1068: system("rm tempgbn")==0 or die die("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAug.pl-1069-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-148-for (my $i=1; $i <= $splitN; $i++){
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl:149: push @dopreds, $i if (!uptodate(["$workDir/shells/aug$i"], ["$workDir/shells/aug$i.out"]) || !`tail aug$i.out | grep command | wc -l`);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-150-}
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-164- print "2 running aug$i\n" if ($verbose >= 2);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl:165: system ("./aug$i");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-166- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-209- if (!uptodate(["$hints"],["$positionWD/hints/hints.gff"])){
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl:210: system("ln -fs $hints $positionWD/hints/hints.gff")==0 or die ("Failed to create hints link.\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-211- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-225- # if (!uptodate([$genome], ["$positionWD/seq/genome.fa"])){
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl:226: # system("ln -fs $genome $$positionWD/seq/genome.fa")==0 or die ("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-227- # print("3 Created a link to $genome with the name genome.fa under $positionWD/seq/\n") if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-244- # calculate minsize
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl:245: my $minsize = `grep -v ">" $genome | wc -c`;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-246- $minsize = int($minsize/$nodeNum)+1;
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-250- print "3 $perlCmdString ..." if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl:251: system("$perlCmdString")==0 or die ("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-252- print "2 The splited fasta files have been placed under $splitDir\n" if ($verbose>=2);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-256-
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl:257: my $splitN = `ls $splitDir/*.fa | wc -l`;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-258- chomp $splitN;
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-279- close AUG;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl:280: system("chmod +x aug$i")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-281- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-344- print "3 rm $out\n" if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl:345: system("rm $out")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-346- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-351- print "3 cat aug$i.out >> $out\n" if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl:352: system("cat aug$i.out >> $out")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl:353: if (`tail aug$i.out | grep command | wc -l` != 1){
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-354- $notfinished++;
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-363- print "3 cat $out | $string > augustus.gff\n" if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl:364: system("cat $out | $string > augustus.gff")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-365-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-369- print "3 $perlCmdString\n" if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl:370: system("$perlCmdString")==0 or die ("failed to execute: $!\n"); # make augustus.aa
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-371- if ( -f "augustus.aa" ) {# may not exist if nothing was predicted
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-385- print "3 mv augustus.gtf ../predictions/\n" if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl:386: system("mv augustus.gtf ../predictions/")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-387- print "3 mv augustus.gff ../predictions/\n" if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl:388: system("mv augustus.gff ../predictions/")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-389-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-397- print "3 $cmdString\n" if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl:398: system("$cmdString")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-399- print "3 mv $gFile ../gbrowse\n" if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl:400: system("mv $gFile ../gbrowse")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-401-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-440- if (! -d $mainDir) {
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl:441: system ("mkdir -p $mainDir");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-442- print "3 Created directory $mainDir.\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-447- for(("gbrowse","shells", "predictions")){mkdir "$_" if (! -d $_);}
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl:448: system ("mkdir -p $position/seq/split");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl:449: system ("mkdir -p $position/hints/");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-450- print "3 All necessary directories have been created under $mainDir\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-470- if(-f "your_job.tmp"){
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl:471: system("rm your_job.tmp")==0 or die ("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-472- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-480- print "3 $cmd\n" if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl:481: system("$cmd")==0 or die ("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-482- $cmd="cat qsub$j.stdout";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl:483: my $output = `$cmd 2>/dev/null`;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-484- print "3 $output" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-494- print "3 rm your_job.tmp\n" if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl:495: system("rm your_job.tmp")==0 or die ("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-496-}
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-509- my $getrunning="ssh $cname \"$clusterENVDefs;${SGEqstatPath}qstat| grep -f $list |wc -l 2>/dev/null\"";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl:510: my $QSTAT_STATUS=`$getrunning`;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-511- $QSTAT_STATUS=~ s/\n//;
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-518- $sleep_now += 30 if ($sleep_now < $sleep_max);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl:519: $QSTAT_STATUS=`$getrunning`;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugPred.pl-520- $QSTAT_STATUS=~ s/\n//;
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-123-}
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:124:system("mkdir -p $workDir");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-125-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-175- print "3 $string\n" if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:176: system("ln -s $trainingset training.gb")==0 or die ("failed to execute: $string\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-177- } elsif ($format eq "gff"){ # if it has GFF format, convert it to Genbank format
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-194- print "3 Running \"$cmdString\" ..." if ($verbose >2);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:195: system("$cmdString")==0 or die("failed to execute $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-196- print " Finished!\n" if ($verbose >2);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-201- print "3 $perlCmdString\n" if ($verbose>2);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:202: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-203- print "3 training.gb with genbank format has been created under $workDir/seq/training/.\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-222- print "2 Running command \"$perlCmdString\" to create AUGUSTUS config files for new species $species\n" if ($verbose>=2);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:223: system("$perlCmdString")==0 or die("Program aborted $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-224- open(NSPECIES, "new_species.stdout") or die ("Cannot open new_species.stdout");
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-271- print "2 Creating training.gb.train and training.gb.test with \"$perlCmdString\"...\n" if ($verbose>=2);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:272: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-273- print "2 Created training.gb.train and training.gb.test under $workDir.\n" if ($verbose>=2);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-293- print "3 $perlCmdString ...\n" if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:294: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:295: system("mv training.gb.train.train training.gb.onlytrain")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-296- print "2 training.gb.train.test and training.gb.onlytrain have been made under $workDir.\n" if ($verbose>=2);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-315- print "2 First try with etraining: etraining --species=$species training.gb.train >train.out ..." if ($verbose>=2);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:316: system("etraining --species=$species training.gb.train 1>train.out 2>train.err")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-317- print " Finished!\n" if ($verbose>=2);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-331- chdir "$workDir/training/" or die ("Can not change directory to $workDir/training.");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:332: system("etraining --species=$species training.gb.train 1>train.out 2>train.err")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-333- print " Finished!\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-358- print "2 First evaluation of parameters ...\n2 Executing \"$cmdString\" ..." if ($verbose>=2);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:359: system("$cmdString")==0 or die("failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-360- print " Finished!\n" if ($verbose>=2);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-378- print "2 Executing \"$cmdString\" ..." if ($verbose>=2);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:379: system("$cmdString")==0 or die("failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-380- print " Finished!\n" if ($verbose>=2);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-390- print "2 Running $cmdString ..." if ($verbose>1);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:391: system("$cmdString")==0 or die("failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-392- print " Finished!\n" if ($verbose>1);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-395- print "2 augustus --species=$species training.gb.test > ./test/augustus.2.withoutCRF.out\n" if ($verbose>1);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:396: system("augustus --species=$species training.gb.test > ./test/augustus.2.withoutCRF.out")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-397- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-411- print "2 cp $_ $_".'.withoutCRF'."\n" if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:412: system("cp $_ $_".'.withoutCRF')==0 or die("failed to execute: cp $_ $_".'.withoutCRF');
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-413- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-422- print "1 Running $cmdString ..." if ($verbose>0);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:423: system("$cmdString")==0 or die("failed to execute: $cmdString!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-424- print " Finished!\n" if ($verbose>0);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-427- print "3 augustus --species=$species training.gb.test > ./test/augustus.2.CRF.out\n" if ($verbose>2);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:428: system("augustus --species=$species training.gb.test > ./test/augustus.2.CRF.out")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-429-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-443- print "2 cp $_ $_".'.CRF'."\n" if ($verbose>1);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:444: system("cp $_ $_".'.CRF')==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-445- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-451- print "3 rm $_\n" if ($verbose >= 3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:452: system("rm $_")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-453- print "3 cp $_".".withoutCRF $_ \n" if ($verbose >= 3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:454: system("cp $_".".withoutCRF $_")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-455- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-498- if (!uptodate(["$positionWD/autoAugPred_hints/predictions/augustus.gtf"],["genemodels.gtf"])){
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:499: system("cp $positionWD/autoAugPred_hints/predictions/augustus.gtf genemodels.gtf");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-500- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-520- print "2 Running command: $perlCmdString ..." if ($verbose>=2);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:521: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-522- print " Finished!\n" if ($verbose>=2);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-530- print "3 Running \"cat utr.gff | perl $string\"..." if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:531: system("cat utr.gff | perl $string > utr.train.gbrowse")==0 or die ("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-532- print " Finished! Made file utr.train.gbrowse\n" if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:533: system("mv utr.train.gbrowse ../../gbrowse")==0 or die ("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-534- print "3 Moved utr.train.gbrowse to $workDir/gbrowse\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-547- close(TRLST);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:548: system("cat tr.lst | sort -u > tr_temp.lst")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:549: system("rm tr.lst")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:550: system("mv tr_temp.lst tr.lst")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-551- open(TR, "tr.lst") or die ("Can not open tr.lst!\n");
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-569- # sort for gff2gbSmallDNA.pl
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:570: system("cat utr.gff genemodels.gtf > genes.gtf_temp")==0 or die ("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-571- open(GENES, "genes.gtf_temp") or die ("Can not open the file genes.gtf_temp");
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-577- close(WRITEGENES);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:578: system("cat genes.gtf_unsort | sort -n -k 4,4 | sort -s -k 10,10 | sort -s -k 1,1 > genes.gtf")==0 or die ("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-579- $string=find("gff2gbSmallDNA.pl");
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-582- print "3 Running \"$perlCmdString\" ..." if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:583: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-584- print " Finished!\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-610- $count=0;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:611: system("cp ../training.gb.train.test t.gb")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-612- open(TEMP2,"t.gb") or die {"Can not open the file t.gb! \n"};
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-623- print "3 Running \"$perlCmdString\"..." if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:624: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-625- print " Finished!\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-627- print "3 Running \"$perlCmdString\"..." if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:628: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-629- print " Finished!\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-639- close(NOMRNA);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:640: system("cat t.nomrna.test.gb bothutr.test.gb.test > train.gb")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-641-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-649- print "1 Have constructed a training set train.gb for UTRs with $counter_gen genes\n" if ($verbose>=1);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:650: system("rm t.gb.train t.gb t.gb.test t.nomrna.test.gb")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:651:# system('grep LOCUS train.gb | perl -pe \'s/^LOCUS\s+(\S+)\s+.*/$1/\' > train.gb.lst')==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-652-# print "3 Made file train.gb.lst under $workDir/training/utr/\n" if ($verbose>=3);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-658-
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:659: system("cp ../training.gb.onlytrain ./")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-660- open(ONLYTRAIN, "training.gb.onlytrain") or die ("Can not open training.gb.onlytrain.");
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-671- close(CDSONLY);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:672: system("rm training.gb.onlytrain")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-673-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-688- $perlCmdString="perl $string remove.lst bothutr.test.gb > train.utronly.gb";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:689: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:690: system("cat cdsonly.gb train.utronly.gb > onlytrain.gb")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-691- print "2 Made onlytrain.gb under $workDir/training/utr/\n" if ($verbose>=2);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-704- close(PARATEMP);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:705: system("rm $paraName")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:706: system("mv cfg_temp $paraName")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-707- chdir "$workDir/training/utr" or die ("Error: could not chdir to $workDir/training/utr!\n");
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-718- print "1 Running \"$perlCmdString\"..." if ($verbose>=1);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:719: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-720- print " finished" if ($verbose>=3);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:721: system("cat train.gb ../training.gb.train > train.all.gb")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-722- } else {
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-727- print "\n2 Running $perlCmdString ..." if ($verbose>=2);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:728: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-729- if ($CRFtrain){
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-730- # TODO: check what is better at the end
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:731: system("etraining --species=$species --UTR=on train.all.gb --CRF=1 1>etrain.out 2>etrain.err")==0 or die("failed to execute: $!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-732- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-833- print "3 $cmdString ..." if ($verbose>2);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:834: system("$cmdString")==0 or die("Program aborted. Possibly \"scipio\" is not installed or not in your PATH");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-835- print "Finished.\n" if ($verbose>2);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-837- print "3 $cmdString ..." if ($verbose>2);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:838: system("$cmdString")==0 or die("Command aborted. Possibly \"scipio\" is not installed or not in your PATH\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-839- print "Finished.\n" if ($verbose>2);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-842- print "3 $cmdString ..." if ($verbose>2);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:843: system("$cmdString")==0 or die("Command aborted.\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-844- print "Finished.\n" if ($verbose>2);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-856- print "3 $perlCmdString\n" if ($verbose>2);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl:857: system("$perlCmdString")==0 or die ("failed to execute: $perlCmdString!\n");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/autoAugTrain.pl-858- print "3 training.gb with genbank format has been created under $workDir/seq/training/.\n" if ($verbose>2);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/checkParamArchive.pl-18-# extract archive
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/checkParamArchive.pl:19:`cd $projectDir; tar xzvf $parArch`;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/checkParamArchive.pl:20:my $speciesName = `ls $projectDir`;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/checkParamArchive.pl-21-chomp($speciesName);
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/createAugustusJoblist.pl-178- close JOB;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/createAugustusJoblist.pl:179: system("chmod +x $jobname");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/createAugustusJoblist.pl-180- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/evalCGP.pl-168-my $gffDir = "tempGFF";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/evalCGP.pl:169:system ("rm -rf $gffDir; mkdir $gffDir");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/evalCGP.pl-170-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/evalCGP.pl-240-if($joingenes){
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/evalCGP.pl:241: system("mv $gffDir/pred.gtf $gffDir/pred.unfiltered.gtf");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/evalCGP.pl:242: system("$cmdpars{'jg_exec_dir'}joingenes $jg_pars -g $gffDir/pred.unfiltered.gtf -o $gffDir/pred.gtf");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/evalCGP.pl-243-}
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/evalCGP.pl-246-# list files that contain the directories of the GTF files being compared (required by eval)
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/evalCGP.pl:247:system ("rm -f $gffDir/annotation_list");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/evalCGP.pl:248:system ("rm -f $gffDir/prediction_list");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/evalCGP.pl-249-foreach my $seq (keys %seqlist) {
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/evalCGP.pl:250: system ("echo '$gffDir/$seq.anno.gtf' >> $gffDir/annotation_list");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/evalCGP.pl:251: system ("echo '$gffDir/$seq.pred.gtf' >> $gffDir/prediction_list");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/evalCGP.pl:252: system ("grep \"^$seq\\b\" $gffDir/pred.gtf > $gffDir/$seq.pred.gtf");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/evalCGP.pl:253: system ("grep \"^$seq\\b\" $gffDir/anno.gtf > $gffDir/$seq.anno.gtf");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/evalCGP.pl-254-}
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/evalCGP.pl-256-# call evaluate_gtf
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/evalCGP.pl:257:system ("$cmdpars{'eval_exec_dir'}evaluate_gtf.pl $gffDir/annotation_list $gffDir/prediction_list");
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/eval_dualdecomp.pl-82-if ($outdir ne ""){
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/eval_dualdecomp.pl:83: system ("rm -rf $outdir; mkdir $outdir");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/eval_dualdecomp.pl-84- $outdir =~ s/([^\/])$/$1\//g;
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/eval_multi_gtf.pl-70-my $dirname = "tempgtf";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/eval_multi_gtf.pl:71:system("rm -rf $dirname; mkdir $dirname");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/eval_multi_gtf.pl-72-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/eval_multi_gtf.pl-85- . "_plus.anno.gtf";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/eval_multi_gtf.pl:86: system($cmdStr);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/eval_multi_gtf.pl-87- $cmdStr = "grep \"^$seq\\b\" $predfilename | grep -P \"\\t\\+\\t\" > "
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/eval_multi_gtf.pl-89- . "_plus.pred.gtf";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/eval_multi_gtf.pl:90: system($cmdStr);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/eval_multi_gtf.pl:91: system( "echo '$dirname/$seq" . "_plus.anno.gtf' >> annotation_list" );
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/eval_multi_gtf.pl:92: system( "echo '$dirname/$seq" . "_plus.pred.gtf' >> prediction_list" );
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/eval_multi_gtf.pl-93- system( "grep \"^$seq\\b\" $annofilename | grep -P \"\\t-\\t\" > "
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/eval_multi_gtf.pl-98- . "_minus.pred.gtf" );
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/eval_multi_gtf.pl:99: system( "echo '$dirname/$seq" . "_minus.anno.gtf' >> annotation_list" );
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/eval_multi_gtf.pl:100: system( "echo '$dirname/$seq" . "_minus.pred.gtf' >> prediction_list" );
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/eval_multi_gtf.pl-101-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/eval_multi_gtf.pl-105-#
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/eval_multi_gtf.pl:106:system( "perl -I $evalpath $evalpath/evaluate_gtf.pl annotation_list prediction_list 2> /dev/null" );
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/eval_multi_gtf.pl-107-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/filterGenesOut_mRNAname.pl-73-#checks whether a gene name exists in reference file
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/filterGenesOut_mRNAname.pl:74:@line = `grep $genename $goodfilename`;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/filterGenesOut_mRNAname.pl-75-if(length($line[0])<1){
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/gbrowseold2gff3.pl-16-
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/gbrowseold2gff3.pl:17:exec("perldoc $0") if ($help);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/gbrowseold2gff3.pl-18-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/gtf2bed.pl-20-
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/gtf2bed.pl:21:exec("perldoc $0") if ($help);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/gtf2bed.pl-22-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/gtf2gff.pl-35-
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/gtf2gff.pl:36:exec("perldoc $0") if ($help || !defined($outfile));
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/gtf2gff.pl-37-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/maf2conswig.pl-32-
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/maf2conswig.pl:33:exec("perldoc $0") if ($help);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/maf2conswig.pl-34-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/new_species.pl-148- }
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/new_species.pl:149: system ("cp $configdir/species/generic/generic_weightmatrix.txt $weightfilename");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/new_species.pl-150-}else{
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/new_species.pl-153- }
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/new_species.pl:154: system ("cp $configdir/species/template_prokaryotic/template_prokaryotic_weightmatrix.txt $weightfilename");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/new_species.pl-155-}
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/new_species.pl-162- }
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/new_species.pl:163: system ("cp $configdir/species/generic/generic_metapars.cfg $metafilename");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/new_species.pl:164: system ("cp $configdir/species/generic/generic_metapars.utr.cfg $metautrfilename");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/new_species.pl:165: system ("cp $configdir/species/generic/generic_metapars.cgp.cfg $metacgpfilename");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/new_species.pl-166-}else{
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/new_species.pl-169- }
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/new_species.pl:170: system ("cp $configdir/species/template_prokaryotic/template_prokaryotic_metapars.cfg $metafilename");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/new_species.pl:171: system ("cp $configdir/species/template_prokaryotic/template_prokaryotic_metapars.utr.cfg $metautrfilename");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/new_species.pl-172-}
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/new_species.pl-179- }
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/new_species.pl:180: system ("cp $configdir/species/template_prokaryotic/template_prokaryotic_ovlp_len.pbl $ovlpfilename");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/new_species.pl-181- print "creating $transshadowfilename ..\n";
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/new_species.pl-184- }
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/new_species.pl:185: system ("cp $configdir/species/template_prokaryotic/template_prokaryotic_trans_shadow_bacterium.pbl $transshadowfilename");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/new_species.pl-186-}
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-393-my $optdir = "tmp_opt_$cmdpars{'species'}";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl:394:system("rm -rf $optdir;mkdir $optdir");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-395-opendir( TMPDIR, $optdir ) or die("Could not open $optdir");
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-475- # make the temporary training and testing files
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl:476: system("rm -f $optdir/curtrain-$k");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-477- for ( my $m = 1; $m <= $cmdpars{"kfold"}; $m++ ) {
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-478- if ( $m != $k ) {
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl:479: system("cat $optdir/bucket$m.gb >> $optdir/curtrain-$k");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-480- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-482- if ( $cmdpars{'onlytrain'} ne '' ) {
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl:483: system("cat $cmdpars{'onlytrain'} >> $optdir/curtrain-$k");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-484- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-660- close(ORIG);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl:661: system("cp $species_cfg_filename $species_cfg_filename.orig$y");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-662- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-996- # delete the temporary training files
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl:997: system("rm -f $optdir/curtrain-$k $optdir/predictions-$k.txt");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-998- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-1002- # make the joint training file (train.gb and onlytrain.gb)
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl:1003: system("rm -f $optdir/curtrain $optdir/curtest");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl:1004: system("cp $cmdpars{'train.gb'} $optdir/curtrain");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-1005- if ( $cmdpars{'onlytrain'} ne '' ) {
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl:1006: system("cat $cmdpars{'onlytrain'} >> $optdir/curtrain");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-1007- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-1014- print "$cmd\n";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl:1015: system($cmd);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl:1016: system("rm -f $optdir/curtrain");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-1017-}
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-1023-if($cmdpars{'cleanup'}==1){
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl:1024: system ("rm -rf $optdir");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-1025-}
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-1072- # make the temporary training and testing files
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl:1073: system("rm -f $optdir/curtrain $optdir/curtest");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl:1074: system("cp $optdir/bucket$k.gb $optdir/curtest");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-1075- for ( my $m = 1; $m <= $cmdpars{"kfold"}; $m++ ) {
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-1076- if ( $m != $k ) {
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl:1077: system("cat $optdir/bucket$m.gb >> $optdir/curtrain");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-1078- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-1080- if ( $cmdpars{'onlytrain'} ne '' ) {
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl:1081: system("cat $cmdpars{'onlytrain'} >> $optdir/curtrain");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-1082- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-1090- .= "$cmdpars{'aug_exec_dir'}etraining --species=$cmdpars{'species'} --AUGUSTUS_CONFIG_PATH=$configdir $argument $pars $be_silent $modelrestrict $optdir/curtrain";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl:1091: system($cmd);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-1092- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-1098- .= "$cmdpars{'aug_exec_dir'}augustus --species=$cmdpars{'species'} --AUGUSTUS_CONFIG_PATH=$configdir $argument $pars $optdir/curtest > $optdir/predictions.txt";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl:1099: system($cmd);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-1100-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-1173- . "$be_silent $modelrestrict $pbloutfiles $optdir/curtrain-$k";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl:1174: system($cmd);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-1175-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-1187- .= "$cmdpars{'aug_exec_dir'}augustus --species=$cmdpars{'species'} --AUGUSTUS_CONFIG_PATH=$configdir $argument $pars $pblinfiles $optdir/bucket$k.gb > $optdir/predictions-$k.txt";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl:1188: system($cmd);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-1189- print "$k ";
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-1259- # this part is done in parallel by the child process
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl:1260: system("rm -rf $optdir/pred$k; mkdir $optdir/pred$k");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-1261- my $cmd = "";
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-1266- .= "$cmdpars{'aug_exec_dir'}augustus --species=$cmdpars{'species'} --AUGUSTUS_CONFIG_PATH=$configdir $argument $pars --alnfile=$optdir/splitMaf/$k.maf --/CompPred/outdir=$optdir/pred$k >$optdir/pred$k/aug.out";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl:1267: system($cmd);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-1268- print "$k ";
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-2042- my $mafDir = "$optdir/splitMaf";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl:2043: system("rm -rf $mafDir; mkdir $mafDir");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-2044-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-2052- { # in the serial case just make a temporary copy of the whole alignment
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl:2053: system("cp $cmdpars{'alnfile'} $mafDir/$cmdpars{'kfold'}.maf");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-2054- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-2122- my $gffDir = "$optdir/tempGFF";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl:2123: system("rm -rf $gffDir; mkdir $gffDir");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-2124-
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-2205- if ($joingenes) {
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl:2206: system("mv $optdir/pred.gtf $optdir/pred.unfiltered.gtf");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-2207- my $cmd = "";
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-2212- .= "$cmdpars{'jg_exec_dir'}joingenes -g $optdir/pred.unfiltered.gtf -o $optdir/pred.gtf";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl:2213: system($cmd);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-2214- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-2217-# list files that contain the directories of the GTF files being compared (required by eval)
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl:2218: system("rm -f $optdir/annotation_list");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl:2219: system("rm -f $optdir/prediction_list");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-2220- foreach my $seq ( keys %seqlist ) {
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl:2221: system("echo '$gffDir/$seq.anno.gtf' >> $optdir/annotation_list");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl:2222: system("echo '$gffDir/$seq.pred.gtf' >> $optdir/prediction_list");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl:2223: system("grep \"^$seq\\b\" $optdir/pred.gtf > $gffDir/$seq.pred.gtf");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl:2224: system("grep \"^$seq\\b\" $optdir/anno.gtf > $gffDir/$seq.anno.gtf");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/optimize_augustus.pl-2225- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/parseSim4Output.pl-116- # let cdbyank use the index to search the sequence
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/parseSim4Output.pl:117: system("echo '$seqname' | cdbyank ${seqfilename}.cidx -d $seqfilename > genomic.fa");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/parseSim4Output.pl-118- system ("perl -i.orig -p -e 's/^Incorrectly.*fixed.\n//' genomic.fa");
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/peptides2alternatives.pl-88- ## map pulled transcripts
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/peptides2alternatives.pl:89: `$blat -t=prot -q=prot -noHead $target $toBeMapped $tmpPsl`;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/peptides2alternatives.pl-90- ## read in psl file, delete already mapped peptides, print psl
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/peptides2alternatives.pl-97- close(PSL) or die "Could not close psl file $tmpPsl!\n";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/peptides2alternatives.pl:98: `rm $toBeMapped`;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/peptides2alternatives.pl-99-}
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/peptides2alternatives.pl-100-print STDERR "Done!\n";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/peptides2alternatives.pl:101:`rm $target $tmpPsl`;
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/pslMap.pl-40-
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/pslMap.pl:41:exec("perldoc $0") if ($help || !defined($infile) || !defined($outfile) || !(defined($mapfile)));
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/pslMap.pl-42-
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augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/runAllSim4.pl-12- $estfilename = shift @f;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/runAllSim4.pl:13: system ("echo '$estfilename' | cdbyank ~/galdieria/galdi3/Newbler_all_454AllContigs.fna.long.uc.cidx > mrna.fa");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/runAllSim4.pl-14- system ("echo '@f' | cdbyank ~/galdieria/galdi3/build3.fa.cidx > genomic.fa");
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augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/runAllSim4.pl-18- close LONG;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/runAllSim4.pl:19: system ("echo '--------\n>$estfilename' >> sim4.results");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/runAllSim4.pl-20- system ("sim4 mrna.fa genomic.fa.long >> sim4.results");
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augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/weedMaf.pl-24-
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/weedMaf.pl:25:exec("perldoc $0") if ($help);
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/weedMaf.pl-26-
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augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/wig2hints.pl-14-if( grep /^--?h$/, @ARGV ) {
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/wig2hints.pl:15: exec("perldoc $0");
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/wig2hints.pl-16-}
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augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-40- ## create the webserver output directory
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl:41: `mkdir $projectWebOutDir`;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-42- if (not(-d "$projectWebOutDir")){
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augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-55- $cmdStr = "cat $head $segmentFile2 $tail > $projectWebOutDir/index.html";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl:56: `$cmdStr`;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-57- unlink $segmentFile2;
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augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-64- my $projectWebOutParams = $wwwOut."/$projectID/$species";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl:65: `mkdir $projectWebOutParams`;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-66- if (not(-d "$projectWebOutParams")){
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augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-155- $cmdStr = "cd $projectWebOutDir; tar -czvf parameters.tar.gz $species &> /dev/null;";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl:156: `$cmdStr`;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-157- }
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augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-176- if(-d $cfgFilesDir){
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl:177: `rm -r $cfgFilesDir`;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-178- print STDERR "Deleting $cfgFilesDir because no relevant parameters can have been produced.\n";4
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augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-181- $cmdStr = "cp $trainingFile $projectWebOutDir/training.gb; cd $projectWebOutDir; gzip training.gb &> /dev/null;";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl:182: `$cmdStr`;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-183- }
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augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-200- $cmdStr = "cp $ab_initio_grailsDir/predictions/* $ab_initio_webDir; cp $ab_initio_grailsDir/gbrowse/* $ab_initio_webDir;";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl:201: `$cmdStr`;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-202- $cmdStr = "cd $projectWebOutDir; tar -czvf ab_initio.tar.gz ab_initio;";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl:203: `$cmdStr`;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-204- $cmdStr = "rm -r $ab_initio_webDir;";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl:205: `$cmdStr`;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-206- }
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augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-221- $cmdStr = "cp $hintsPred_grailsDir/predictions/* $hintsPred_webDir; cp $hintsPred_grailsDir/gbrowse/* $hintsPred_webDir;";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl:222: `$cmdStr`;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-223- $cmdStr = "cd $projectWebOutDir; tar -czvf hints_pred.tar.gz hints_pred;";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl:224: `$cmdStr`;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-225- $cmdStr = "rm -r $hintsPred_webDir;";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl:226: `$cmdStr`;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-227- }
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augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-240- $cmdStr = "cp $utrPred_grailsDir/predictions/* $utrPred_webDir; cp $utrPred_grailsDir/gbrowse/* $utrPred_webDir;";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl:241: `$cmdStr`;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-242- $cmdStr = "cd $projectWebOutDir; tar -czvf utr_pred.tar.gz utr_pred;";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl:243: `$cmdStr`;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-244- $cmdStr = "rm -r $utrPred_webDir;";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl:245: `$cmdStr`;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-246- }
##############################################
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-260- $cmdStr = "cp $utrHintsPred_grailsDir/predictions/* $utrHintsPred_webDir; cp $utrHintsPred_grailsDir/gbrowse/* $utrHintsPred_webDir;";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl:261: `$cmdStr`;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-262- $cmdStr = "cd $projectWebOutDir; tar -czvf hints_utr_pred.tar.gz hints_utr_pred;";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl:263: `$cmdStr`;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-264- $cmdStr = "rm -r $utrHintsPred_webDir;";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl:265: `$cmdStr`;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-266- }
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augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-273- $cmdStr = "cp $errorFile $projectWebOutDir; cp $logFile $projectWebOutDir;";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl:274: `$cmdStr`;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-275- }else{
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augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-284- $cmdStr = "cd $grailsOut/$projectID; tar -czvf predictions.tar.gz augustus;";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl:285: `$cmdStr`;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-286- $cmdStr = "cp $grailsOut/$projectID/predictions.tar.gz $projectWebOutDir/predictions.tar.gz";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl:287: `$cmdStr`;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-288- }
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augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-350-$cmdStr = "cat $head $segmentFile2 $tail > $projectWebOutDir/index.html";
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl:351:`$cmdStr`;
augustus-3.3.3+dfsg/.pc/interpreter_paths.patch/scripts/writeResultsPage.pl-352-unlink $segmentFile2;