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_________________ __ __ __| _/|__|/ |_
/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
proteinortho-6.0.24+dfsg/README.md-120-
proteinortho-6.0.24+dfsg/README.md:121: ```docker run --rm --mount "type=bind,src=/home/$(id -un),dst=/home/$(id -un)" -u $(id -u):$(id -g) -it quay.io/biocontainers/proteinortho:6.0.22--hfd40d39_0 bash```
proteinortho-6.0.24+dfsg/README.md-122-
##############################################
proteinortho-6.0.24+dfsg/proteinortho-752- if(! -d $tmp_path."/proteinortho_cache_$project"){
proteinortho-6.0.24+dfsg/proteinortho:753: system("mkdir $tmp_path/proteinortho_cache_$project");
proteinortho-6.0.24+dfsg/proteinortho-754- if( -d $tmp_path."/proteinortho_cache_$project"){
##############################################
proteinortho-6.0.24+dfsg/proteinortho-812- if($prefix eq $i_withoutEnd){
proteinortho-6.0.24+dfsg/proteinortho:813: system("cp $files[$i] $tmp_path/".basename($files[$i])."; if [ ! -z \"\$(tail -c 1 \"$tmp_path/".basename($files[$i])."\")\" ]; then echo '' >> $tmp_path/".basename($files[$i])."; fi; cat ".$files[$j]." >>$tmp_path/".basename($files[$i]));
proteinortho-6.0.24+dfsg/proteinortho-814- push(@new_files,"$tmp_path/".basename($files[$i]));
##############################################
proteinortho-6.0.24+dfsg/proteinortho-860- } else {
proteinortho-6.0.24+dfsg/proteinortho:861: print STDERR "ps --forest -o pid,tty,stat,time,cmd -g $masterpid\n".`ps --forest -o pid,tty,stat,time,cmd -g $masterpid`."\n";
proteinortho-6.0.24+dfsg/proteinortho-862- }
##############################################
proteinortho-6.0.24+dfsg/proteinortho-873- foreach my $file (keys %gene_counter) {
proteinortho-6.0.24+dfsg/proteinortho:874: if($blastmode !~ m/blat/ && `ls '${file}'.${blastmode}* 1>/dev/null 2>&1` ne ""){ # test here
proteinortho-6.0.24+dfsg/proteinortho-875- my $a = "$tmp_path/DB/".basename($file);
proteinortho-6.0.24+dfsg/proteinortho:876: if(`ls '${a}'.${blastmode}* 1>/dev/null 2>&1` ne ""){ # or here
proteinortho-6.0.24+dfsg/proteinortho-877- &Error("I did not find the database for ".$_[0]." (".$a."). Did you run --step=1 and maybe removed the databases? Please rerun 'proteinortho --step=1 --force /path/to/fastas' such that the databases can be recreated and then proceed with -step=2 and -step=3.");
##############################################
proteinortho-6.0.24+dfsg/proteinortho-897- if($synteny){
proteinortho-6.0.24+dfsg/proteinortho:898: system("$po_path/proteinortho_cleanupblastgraph $syngraph"."* >tmp_$syngraph 2>/dev/null && mv tmp_$syngraph $syngraph"."_clean");
proteinortho-6.0.24+dfsg/proteinortho-899- $syngraph.="_clean";
##############################################
proteinortho-6.0.24+dfsg/proteinortho-901- }else{
proteinortho-6.0.24+dfsg/proteinortho:902: system("$po_path/proteinortho_cleanupblastgraph $simgraph"."* >tmp_$simgraph 2>/dev/null && mv tmp_$simgraph $simgraph"."_clean");
proteinortho-6.0.24+dfsg/proteinortho-903- $simgraph.="_clean";
##############################################
proteinortho-6.0.24+dfsg/proteinortho-921-#clean up tmp dir
proteinortho-6.0.24+dfsg/proteinortho:922:if (!$keep && $tmp_path =~ m/\/proteinortho_cache_[^\/]+\d*\/$/ && $step!=1){system("rm -r $tmp_path >/dev/null 2>&1");}
proteinortho-6.0.24+dfsg/proteinortho-923-
##############################################
proteinortho-6.0.24+dfsg/proteinortho-932- foreach my $file (@files) {
proteinortho-6.0.24+dfsg/proteinortho:933: system("rm $file.$blastmode"."*");
proteinortho-6.0.24+dfsg/proteinortho-934- }
##############################################
proteinortho-6.0.24+dfsg/proteinortho-978- if($verbose == 2){ $cluster_verbose_level = "-debug 1 "; }
proteinortho-6.0.24+dfsg/proteinortho:979: system ("OMP_PROC_BIND=$ompprocbind $po_path/proteinortho_clustering $cluster_verbose_level -minspecies $minspecies -ram ".$freemem_inMB." -kmere ".(1-$exactstep3)." -debug $debug -cpus $cpus -weighted 1 -conn $connectivity -purity $purity $clusterOptions -rmgraph '$rm_simgraph' $simgraph* >'$simtable'");
proteinortho-6.0.24+dfsg/proteinortho-980- if ($? != 0) {
##############################################
proteinortho-6.0.24+dfsg/proteinortho-983- }else{
proteinortho-6.0.24+dfsg/proteinortho:984: my $stderrout = `$po_path/proteinortho_do_mcl.pl $cpus $simgraph*`;
proteinortho-6.0.24+dfsg/proteinortho-985- if ($? != 0) {
##############################################
proteinortho-6.0.24+dfsg/proteinortho-988- }
proteinortho-6.0.24+dfsg/proteinortho:989: system("mv mcl.proteinortho $simtable");
proteinortho-6.0.24+dfsg/proteinortho:990: system("mv mcl.proteinortho-graph $csimgraph");
proteinortho-6.0.24+dfsg/proteinortho-991- }
##############################################
proteinortho-6.0.24+dfsg/proteinortho-997-
proteinortho-6.0.24+dfsg/proteinortho:998: system("(head -n 1 '$simtable' && tail -n +2 '$simtable' | sort -k1,2nr -k3,3gr ) > '$simtable.sort'; mv '$simtable.sort' '$simtable'");
proteinortho-6.0.24+dfsg/proteinortho-999-
##############################################
proteinortho-6.0.24+dfsg/proteinortho-1002- my $fastas = "'".join("' '",@files)."'";
proteinortho-6.0.24+dfsg/proteinortho:1003: system("$po_path/proteinortho_singletons.pl $fastas <'$simtable' >>'$simtable'");
proteinortho-6.0.24+dfsg/proteinortho-1004- }
##############################################
proteinortho-6.0.24+dfsg/proteinortho-1007- if (!$nograph && !$useMcl) {
proteinortho-6.0.24+dfsg/proteinortho:1008: system("$po_path/proteinortho_graphMinusRemovegraph '$rm_simgraph' $simgraph* >'$csimgraph'");
proteinortho-6.0.24+dfsg/proteinortho-1009- unless ($keep) {unlink($rm_simgraph);}
##############################################
proteinortho-6.0.24+dfsg/proteinortho-1015- if(-x "$po_path/proteinortho_summary.pl"){
proteinortho-6.0.24+dfsg/proteinortho:1016: system("$po_path/proteinortho_summary.pl '$csimgraph' >>'$csimgraph.summary' 2>/dev/null");
proteinortho-6.0.24+dfsg/proteinortho-1017- }
##############################################
proteinortho-6.0.24+dfsg/proteinortho-1021- if(scalar @files < 10){
proteinortho-6.0.24+dfsg/proteinortho:1022: system("perl $po_path/proteinortho2html.pl $simtable '".join("' '",@files)."' >$simtablehtml");
proteinortho-6.0.24+dfsg/proteinortho-1023- if($verbose){print STDERR "[OUTPUT] -> Orthologous groups are written to $simtablehtml\n";}
##############################################
proteinortho-6.0.24+dfsg/proteinortho-1028- if ($doxml) {
proteinortho-6.0.24+dfsg/proteinortho:1029: system("perl $po_path/proteinortho2xml.pl $simtable >$simtable.xml");
proteinortho-6.0.24+dfsg/proteinortho:1030: if ($? != 0) {system("rm $simtable.xml"); &Error("proteinortho2xml.pl failed");}
proteinortho-6.0.24+dfsg/proteinortho-1031- if($verbose){print STDERR "[OUTPUT] -> Generated the ortho-xml file $simtable.xml";}
##############################################
proteinortho-6.0.24+dfsg/proteinortho-1042- if($verbose == 2){ $cluster_verbose_level = "-debug 1 "; }
proteinortho-6.0.24+dfsg/proteinortho:1043: system ("OMP_PROC_BIND=$ompprocbind $po_path/proteinortho_clustering $cluster_verbose_level $clusterOptions -minspecies $minspecies -ram ".$freemem_inMB." -kmere ".(1-$exactstep3)." -debug $debug -cpus $cpus -weighted 1 -conn $connectivity -purity $purity $clusterOptions -rmgraph '$rm_syngraph' $syngraph* >'$syntable'");
proteinortho-6.0.24+dfsg/proteinortho-1044- if ($? != 0) {
##############################################
proteinortho-6.0.24+dfsg/proteinortho-1047- }else{
proteinortho-6.0.24+dfsg/proteinortho:1048: system($po_path.'/proteinortho_do_mcl.pl '.$cpus.' '.$syngraph.'*');
proteinortho-6.0.24+dfsg/proteinortho:1049: system("mv mcl.proteinortho $syntable");
proteinortho-6.0.24+dfsg/proteinortho:1050: system("mv mcl.proteinortho-graph $csyngraph");
proteinortho-6.0.24+dfsg/proteinortho-1051- }
proteinortho-6.0.24+dfsg/proteinortho-1052-
proteinortho-6.0.24+dfsg/proteinortho:1053: system("(head -n 1 '$syntable' && tail -n +2 '$syntable' | sort -k1,2nr -k3,3gr ) > '$syntable.sort'; mv '$syntable.sort' '$syntable'");
proteinortho-6.0.24+dfsg/proteinortho-1054-
##############################################
proteinortho-6.0.24+dfsg/proteinortho-1059- my $fastas = "'".join("' '",@files)."'";
proteinortho-6.0.24+dfsg/proteinortho:1060: system("$po_path/proteinortho_singletons.pl $fastas <'$syntable' >>'$syntable'");
proteinortho-6.0.24+dfsg/proteinortho-1061- }
##############################################
proteinortho-6.0.24+dfsg/proteinortho-1063- if (!$nograph && !$useMcl) {
proteinortho-6.0.24+dfsg/proteinortho:1064: system("$po_path/proteinortho_graphMinusRemovegraph '$rm_syngraph' $syngraph* >'$csyngraph'");
proteinortho-6.0.24+dfsg/proteinortho-1065- unless ($keep) {unlink($rm_syngraph);}
##############################################
proteinortho-6.0.24+dfsg/proteinortho-1070- if(-x "$po_path/proteinortho_summary.pl"){
proteinortho-6.0.24+dfsg/proteinortho:1071: system("$po_path/proteinortho_summary.pl '$csyngraph' >>'$csyngraph.summary'");
proteinortho-6.0.24+dfsg/proteinortho-1072- }
##############################################
proteinortho-6.0.24+dfsg/proteinortho-1074-
proteinortho-6.0.24+dfsg/proteinortho:1075: system("perl $po_path/proteinortho2html.pl $syntable '".join("' '",@files)."' >$syntablehtml");
proteinortho-6.0.24+dfsg/proteinortho-1076- if($verbose){print STDERR "[OUTPUT] -> Orthologous groups are written to $syntablehtml\n";}
##############################################
proteinortho-6.0.24+dfsg/proteinortho-1078- if ($doxml) {
proteinortho-6.0.24+dfsg/proteinortho:1079: system("perl $po_path/proteinortho2xml.pl $syntable >$syntable.xml");
proteinortho-6.0.24+dfsg/proteinortho:1080: if ($? != 0) {system("rm $syntable.xml"); &Error("$ORANGE\n[WARNING]$NC -> proteinortho2xml.pl failed");}
proteinortho-6.0.24+dfsg/proteinortho-1081- if($verbose){print STDERR "[OUTPUT] -> Generated the ortho-xml file $syntable.xml";}
##############################################
proteinortho-6.0.24+dfsg/proteinortho-1447- print STDERR "\n$RED [Error] Failed to run $po_path/proteinortho_ffadj_mcs.py for\n$file_i vs $file_j\nMoving source to $temp_file.err for debugging\nI will continue, but results may be insufficient.$NC \n\n";
proteinortho-6.0.24+dfsg/proteinortho:1448: system("mv $temp_file.tmp $temp_file.err");
proteinortho-6.0.24+dfsg/proteinortho-1449- next;
##############################################
proteinortho-6.0.24+dfsg/proteinortho-1893-
proteinortho-6.0.24+dfsg/proteinortho:1894: if(!$force && `ls '${file}'.${blastmode}* 1>/dev/null 2>&1` ne ""){
proteinortho-6.0.24+dfsg/proteinortho-1895- if ($verbose) {print STDERR "The database for '$file' is present and will be used\n";}
##############################################
proteinortho-6.0.24+dfsg/proteinortho-1897- if ($verbose) {print STDERR "Building database for '$file'\t(".$gene_counter{$file}." sequences)\n";}
proteinortho-6.0.24+dfsg/proteinortho:1898: system("$makedb -d '$file' -n '$file.$blastmode' >\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho-1899- if ($? != 0) {print STDERR ("$ORANGE\n[WARNING]$NC ".$blastmode." failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in $tmp_path (-tmp)."); if($step==1){print STDERR "$ORANGE Please ensure that you use -tmp=$tmp_path -keep (and use the same -project= name) for future analysis.$NC";}print "\n";
##############################################
proteinortho-6.0.24+dfsg/proteinortho-1902- if($step==1){$oldkeep=$keep;$keep=1;}
proteinortho-6.0.24+dfsg/proteinortho:1903: system("$makedb -d '$file' -n '$tmp_path/DB/".basename($file).".$blastmode' >\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho:1904: system("ln -s '".abs_path($file)."' '$tmp_path/DB/".basename($file)."'");
proteinortho-6.0.24+dfsg/proteinortho-1905-
##############################################
proteinortho-6.0.24+dfsg/proteinortho-1914-
proteinortho-6.0.24+dfsg/proteinortho:1915: if(!$force && `ls '${file}'.${blastmode}* 1>/dev/null 2>&1` ne ""){
proteinortho-6.0.24+dfsg/proteinortho-1916- if ($verbose) {print STDERR "The database for '$file' is present and will be used\n";}
##############################################
proteinortho-6.0.24+dfsg/proteinortho-1918- if ($verbose) {print STDERR "Building database for '$file'\t(".$gene_counter{$file}." sequences)\n";}
proteinortho-6.0.24+dfsg/proteinortho:1919: system("$makedb '$file' -d '$file.$blastmode' --quiet >\/dev\/null 2>\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho-1920- if ($? != 0) {print STDERR ("$ORANGE\n[WARNING]$NC ".$blastmode." failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in $tmp_path (-tmp)."); if($step==1){print STDERR "$ORANGE Please ensure that you use -tmp=$tmp_path -keep (and use the same -project= name) for future analysis.$NC";}print "\n";
##############################################
proteinortho-6.0.24+dfsg/proteinortho-1923- if($step==1){$oldkeep=$keep;$keep=1;}
proteinortho-6.0.24+dfsg/proteinortho:1924: system("$makedb '$file' -d '$tmp_path/DB/".basename($file).".$blastmode' --quiet >\/dev\/null 2>\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho:1925: system("ln -s '".abs_path($file)."' '$tmp_path/DB/".basename($file)."'");
proteinortho-6.0.24+dfsg/proteinortho-1926-
##############################################
proteinortho-6.0.24+dfsg/proteinortho-1936-
proteinortho-6.0.24+dfsg/proteinortho:1937: if(!$force && `ls '${file}'.${blastmode}* 1>/dev/null 2>&1` ne ""){
proteinortho-6.0.24+dfsg/proteinortho-1938- if ($verbose) {print STDERR "The database for '$file' is present and will be used\n";}
##############################################
proteinortho-6.0.24+dfsg/proteinortho-1940- if ($verbose) {print STDERR "Building database for '$file'\t(".$gene_counter{$file}." sequences)\n";}
proteinortho-6.0.24+dfsg/proteinortho:1941: system("$makedb index -f '$file' -p '$file.$blastmode' >\/dev\/null 2>\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho-1942- if ($? != 0) {print STDERR ("$ORANGE\n[WARNING]$NC ".$blastmode." failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in $tmp_path (-tmp)."); if($step==1){print STDERR "$ORANGE Please ensure that you use -tmp=$tmp_path -keep (and use the same -project= name) for future analysis.$NC";}print "\n";
##############################################
proteinortho-6.0.24+dfsg/proteinortho-1945- if($step==1){$oldkeep=$keep;$keep=1;}
proteinortho-6.0.24+dfsg/proteinortho:1946: system("$makedb index -f '$file' -p '$tmp_path/DB/".basename($file).".$blastmode' >\/dev\/null 2>\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho:1947: system("ln -s '".abs_path($file)."' '$tmp_path/DB/".basename($file)."'");
proteinortho-6.0.24+dfsg/proteinortho-1948-
##############################################
proteinortho-6.0.24+dfsg/proteinortho-1957-
proteinortho-6.0.24+dfsg/proteinortho:1958: if(!$force && `ls '${file}'.${blastmode}* 1>/dev/null 2>&1` ne ""){
proteinortho-6.0.24+dfsg/proteinortho-1959- if ($verbose) {print STDERR "The database for '$file' is present and will be used\n";}
##############################################
proteinortho-6.0.24+dfsg/proteinortho-1961- if ($verbose) {print STDERR "Building database for '$file'\t(".$gene_counter{$file}." sequences)\n";}
proteinortho-6.0.24+dfsg/proteinortho:1962: system("$makedb --dbtype 1 '$file' '$file.$blastmode' >\/dev\/null 2>\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho-1963- if ($? != 0) {print STDERR ("$ORANGE\n[WARNING]$NC ".$blastmode." failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in $tmp_path (-tmp)."); if($step==1){print STDERR "$ORANGE Please ensure that you use -tmp=$tmp_path -keep (and use the same -project= name) for future analysis.$NC";}print "\n";
##############################################
proteinortho-6.0.24+dfsg/proteinortho-1966- if($step==1){$oldkeep=$keep;$keep=1;}
proteinortho-6.0.24+dfsg/proteinortho:1967: system("$makedb --dbtype 1 '$file' '$tmp_path/DB/".basename($file).".$blastmode' >\/dev\/null 2>\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho:1968: system("ln -s '".abs_path($file)."' '$tmp_path/DB/".basename($file)."'");
proteinortho-6.0.24+dfsg/proteinortho-1969-
##############################################
proteinortho-6.0.24+dfsg/proteinortho-1979-
proteinortho-6.0.24+dfsg/proteinortho:1980: if(!$force && `ls '${file}'.${blastmode}* 1>/dev/null 2>&1` ne ""){
proteinortho-6.0.24+dfsg/proteinortho-1981- if ($verbose) {print STDERR "The database for '$file' is present and will be used\n";}
##############################################
proteinortho-6.0.24+dfsg/proteinortho-1983- if ($verbose) {print STDERR "Building database for '$file'\t(".$gene_counter{$file}." sequences)\n";}
proteinortho-6.0.24+dfsg/proteinortho:1984: system("$makedb --dbtype 2 '$file' '$file.$blastmode' >\/dev\/null 2>\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho-1985- if ($? != 0) {print STDERR ("$ORANGE\n[WARNING]$NC ".$blastmode." failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in $tmp_path (-tmp)."); if($step==1){print STDERR "$ORANGE Please ensure that you use -tmp=$tmp_path -keep (and use the same -project= name) for future analysis.$NC";}print "\n";
##############################################
proteinortho-6.0.24+dfsg/proteinortho-1988- if($step==1){$oldkeep=$keep;$keep=1;}
proteinortho-6.0.24+dfsg/proteinortho:1989: system("$makedb --dbtype 2 '$file' '$tmp_path/DB/".basename($file).".$blastmode' >\/dev\/null 2>\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho:1990: system("ln -s '".abs_path($file)."' '$tmp_path/DB/".basename($file)."'");
proteinortho-6.0.24+dfsg/proteinortho-1991-
##############################################
proteinortho-6.0.24+dfsg/proteinortho-2001-
proteinortho-6.0.24+dfsg/proteinortho:2002: if(!$force && `ls '${file}'.${blastmode}* 1>/dev/null 2>&1` ne ""){
proteinortho-6.0.24+dfsg/proteinortho-2003- if ($verbose) {print STDERR "The database for '$file' is present and will be used\n";}
##############################################
proteinortho-6.0.24+dfsg/proteinortho-2005- if ($verbose) {print STDERR "Building database for '$file'\t(".$gene_counter{$file}." sequences)\n";}
proteinortho-6.0.24+dfsg/proteinortho:2006: system("$makedb '$file' -output '$file.$blastmode' >\/dev\/null 2>\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho-2007- if ($? != 0) {print STDERR ("$ORANGE\n[WARNING]$NC ".$blastmode." failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in $tmp_path (-tmp)."); if($step==1){print STDERR "$ORANGE Please ensure that you use -tmp=$tmp_path -keep (and use the same -project= name) for future analysis.$NC";}print "\n";
##############################################
proteinortho-6.0.24+dfsg/proteinortho-2010- if($step==1){$oldkeep=$keep;$keep=1;}
proteinortho-6.0.24+dfsg/proteinortho:2011: system("$makedb '$file' -output '$tmp_path/DB/".basename($file).".$blastmode' >\/dev\/null 2>\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho:2012: system("ln -s '".abs_path($file)."' '$tmp_path/DB/".basename($file)."'");
proteinortho-6.0.24+dfsg/proteinortho-2013-
##############################################
proteinortho-6.0.24+dfsg/proteinortho-2022-
proteinortho-6.0.24+dfsg/proteinortho:2023: if(!$force && `ls '${file}'.${blastmode}* 1>/dev/null 2>&1` ne ""){
proteinortho-6.0.24+dfsg/proteinortho-2024- if ($verbose) {print STDERR "The database for '$file' is present and will be used\n";}
##############################################
proteinortho-6.0.24+dfsg/proteinortho-2027- if($blastmode eq "lastp"){
proteinortho-6.0.24+dfsg/proteinortho:2028: system("$makedb -p '$file.$blastmode' '$file'");
proteinortho-6.0.24+dfsg/proteinortho-2029- if ($? != 0) {print STDERR ("$ORANGE\n[WARNING]$NC ".$blastmode." failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in $tmp_path (-tmp)."); if($step==1){print STDERR "$ORANGE Please ensure that you use -tmp=$tmp_path -keep (and use the same -project= name) for future analysis.$NC";}print "\n";
##############################################
proteinortho-6.0.24+dfsg/proteinortho-2032- if($step==1){$oldkeep=$keep;$keep=1;}
proteinortho-6.0.24+dfsg/proteinortho:2033: system("$makedb -p '$tmp_path/DB/".basename($file).".$blastmode' '$file'");
proteinortho-6.0.24+dfsg/proteinortho:2034: system("ln -s '".abs_path($file)."' '$tmp_path/DB/".basename($file)."'");
proteinortho-6.0.24+dfsg/proteinortho-2035-
##############################################
proteinortho-6.0.24+dfsg/proteinortho-2038- }else{
proteinortho-6.0.24+dfsg/proteinortho:2039: system("$makedb '$file.$blastmode' '$file'");
proteinortho-6.0.24+dfsg/proteinortho-2040- if ($? != 0) {print STDERR ("$ORANGE\n[WARNING]$NC ".$blastmode." failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in $tmp_path (-tmp)."); if($step==1){print STDERR "$ORANGE Please ensure that you use -tmp=$tmp_path -keep (and use the same -project= name) for future analysis.$NC";}print "\n";
##############################################
proteinortho-6.0.24+dfsg/proteinortho-2043- if($step==1){$oldkeep=$keep;$keep=1;}
proteinortho-6.0.24+dfsg/proteinortho:2044: system("$makedb '$tmp_path/DB/".basename($file).".$blastmode' '$file'");
proteinortho-6.0.24+dfsg/proteinortho:2045: system("ln -s '".abs_path($file)."' '$tmp_path/DB/".basename($file)."'");
proteinortho-6.0.24+dfsg/proteinortho-2046-
##############################################
proteinortho-6.0.24+dfsg/proteinortho-2059-
proteinortho-6.0.24+dfsg/proteinortho:2060: if(!$force && `ls '${file}'.${blastmode}* 1>/dev/null 2>&1` ne ""){
proteinortho-6.0.24+dfsg/proteinortho-2061- if ($verbose) {print STDERR "The database for '$file' is present and will be used\n";}
##############################################
proteinortho-6.0.24+dfsg/proteinortho-2064- if ($debug) {print STDERR "$makedb '$file' -out '$file.$blastmode' >\/dev\/null\n";}
proteinortho-6.0.24+dfsg/proteinortho:2065: system("$makedb '$file' -out '$file.$blastmode' >\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho-2066- if ($? != 0) {print STDERR ("$ORANGE\n[WARNING]$NC ".$blastmode." failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in $tmp_path (-tmp)."); if($step==1){print STDERR "$ORANGE Please ensure that you use -tmp=$tmp_path -keep (and use the same -project= name) for future analysis.$NC";}print "\n";
##############################################
proteinortho-6.0.24+dfsg/proteinortho-2069- if($step==1){$oldkeep=$keep;$keep=1;}
proteinortho-6.0.24+dfsg/proteinortho:2070: system("$makedb '$file' -out '$tmp_path/DB/".basename($file).".$blastmode' >\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho-2071-
##############################################
proteinortho-6.0.24+dfsg/proteinortho-2079-
proteinortho-6.0.24+dfsg/proteinortho:2080: if(!$force && `ls '${file}'.${blastmode}* 1>/dev/null 2>&1` ne ""){
proteinortho-6.0.24+dfsg/proteinortho-2081- if ($verbose) {print STDERR "The database for '$file' is present and will be used\n";}
##############################################
proteinortho-6.0.24+dfsg/proteinortho-2088- if ($debug) {print STDERR "$makedb -dbtype ".$autoblast_fileis{$file}." -in '$file' -out '$file.$blastmode' >\/dev\/null\n";}
proteinortho-6.0.24+dfsg/proteinortho:2089: system("$makedb -dbtype ".$autoblast_fileis{$file}." -in '$file' -out '$file.$blastmode' >\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho-2090- if ($? != 0) {print STDERR ("$ORANGE\n[WARNING]$NC ".$blastmode." failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in $tmp_path (-tmp)."); if($step==1){print STDERR "$ORANGE Please ensure that you use -tmp=$tmp_path -keep (and use the same -project= name) for future analysis.$NC";}print "\n";
##############################################
proteinortho-6.0.24+dfsg/proteinortho-2093- if($step==1){$oldkeep=$keep;$keep=1;}
proteinortho-6.0.24+dfsg/proteinortho:2094: system("$makedb '$file' -out '$tmp_path/DB/".basename($file).".$blastmode' >\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho-2095-
##############################################
proteinortho-6.0.24+dfsg/proteinortho-2103-
proteinortho-6.0.24+dfsg/proteinortho:2104: if(!$force && `ls '${file}'.${blastmode}* 1>/dev/null 2>&1` ne ""){
proteinortho-6.0.24+dfsg/proteinortho-2105- if ($verbose) {print STDERR "The database for '$file' is present and will be used\n";}
##############################################
proteinortho-6.0.24+dfsg/proteinortho-2108- if ($debug) {print STDERR "$makedb '$file' -out '$file.$blastmode' >\/dev\/null\n";}
proteinortho-6.0.24+dfsg/proteinortho:2109: system("$makedb '$file' -n '$file.$blastmode' >\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho-2110- if ($? != 0) {print STDERR ("$ORANGE\n[WARNING]$NC ".$blastmode." failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in $tmp_path (-tmp)."); if($step==1){print STDERR "$ORANGE Please ensure that you use -tmp=$tmp_path -keep (and use the same -project= name) for future analysis.$NC";}print "\n";
##############################################
proteinortho-6.0.24+dfsg/proteinortho-2113- if($step==1){$oldkeep=$keep;$keep=1;}
proteinortho-6.0.24+dfsg/proteinortho:2114: system("$makedb '$file' -n '$tmp_path/DB/".basename($file).".$blastmode' >\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho-2115-
##############################################
proteinortho-6.0.24+dfsg/proteinortho-2205- if ($blastmode eq "diamond") {
proteinortho-6.0.24+dfsg/proteinortho:2206: @data=`$command`; # run diamond
proteinortho-6.0.24+dfsg/proteinortho-2207- if ($? != 0) {&Error($blastmode." failed with code $?.$NC (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)\nThe most common sources of this error are:\n- no space left on device error.\n- outdated $blastmode, please update $blastmode or consider another -p algorithm.\n- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'\n- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for $blastmode? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.");}
proteinortho-6.0.24+dfsg/proteinortho-2208- if($debug eq "test_sort"){while (<"$bla.tmp">){if ($_ =~ /[^\t]+([,])[^\t]+[eE]/) {print "found forbidden symbol '$1' at $_ in $bla\n";&reset_locale();die;}}}
proteinortho-6.0.24+dfsg/proteinortho:2209: if($keep){system("mv '$bla.tmp' '$bla'");}
proteinortho-6.0.24+dfsg/proteinortho-2210-
##############################################
proteinortho-6.0.24+dfsg/proteinortho-2212-
proteinortho-6.0.24+dfsg/proteinortho:2213: system("$command");
proteinortho-6.0.24+dfsg/proteinortho-2214- if ($? != 0) {&Error($blastmode." failed with code $?.$NC (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)\nThe most common sources of this error are:\n- no space left on device error.\n- outdated $blastmode, please update $blastmode or consider another -p algorithm.\n- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'\n- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for $blastmode? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.");}
##############################################
proteinortho-6.0.24+dfsg/proteinortho-2220- unlink "$bla.aln"; #remove aln file
proteinortho-6.0.24+dfsg/proteinortho:2221: system("tail -n +6 '$bla.m82' >'$bla'"); # remove head/comment lines of rapsearch
proteinortho-6.0.24+dfsg/proteinortho-2222- unlink '$bla.m82';
##############################################
proteinortho-6.0.24+dfsg/proteinortho-2226-
proteinortho-6.0.24+dfsg/proteinortho:2227: system("$command");
proteinortho-6.0.24+dfsg/proteinortho-2228- if ($? != 0) {&Error($blastmode." failed with code $?.$NC (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)\nThe most common sources of this error are:\n- no space left on device error.\n- outdated $blastmode, please update $blastmode or consider another -p algorithm.\n- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'\n- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for $blastmode? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.");}
proteinortho-6.0.24+dfsg/proteinortho-2229- if($debug eq "test_sort"){while (<"$bla.tmp">){if ($_ =~ /[^\t]+([,])[^\t]+[eE]/) {print "found forbidden symbol '$1' at $_ in $bla\n";&reset_locale();die;}}}
proteinortho-6.0.24+dfsg/proteinortho:2230: system("perl $po_path/proteinortho_formatUsearch.pl '$bla.tmp' >'$bla'"); # problem with ublast/usearch: gene names include the description.
proteinortho-6.0.24+dfsg/proteinortho-2231- unlink "$bla.tmp";
##############################################
proteinortho-6.0.24+dfsg/proteinortho-2234-
proteinortho-6.0.24+dfsg/proteinortho:2235: system("$command");
proteinortho-6.0.24+dfsg/proteinortho-2236- if ($? != 0) {&Error($blastmode." failed with code $?.$NC (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)\nThe most common sources of this error are:\n- no space left on device error.\n- outdated $blastmode, please update $blastmode or consider another -p algorithm.\n- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'\n- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for $blastmode? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.");}
proteinortho-6.0.24+dfsg/proteinortho-2237- if($debug eq "test_sort"){while (<"$bla.tmp">){if ($_ =~ /[^\t]+([,])[^\t]+[eE]/) {print "found forbidden symbol '$1' at $_ in $bla\n";&reset_locale();die;}}}
proteinortho-6.0.24+dfsg/proteinortho:2238: system("tail -n +2 '$bla.tmp' > '$bla'");
proteinortho-6.0.24+dfsg/proteinortho-2239- unlink "timing.txt";
##############################################
proteinortho-6.0.24+dfsg/proteinortho-2243-
proteinortho-6.0.24+dfsg/proteinortho:2244: system("$command");
proteinortho-6.0.24+dfsg/proteinortho-2245- if ($? != 0) {&Error($blastmode." failed with code $?.$NC (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)\nThe most common sources of this error are:\n- no space left on device error.\n- outdated $blastmode, please update $blastmode or consider another -p algorithm.\n- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'\n- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for $blastmode? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.");}
proteinortho-6.0.24+dfsg/proteinortho-2246- if($debug eq "test_sort"){while (<"$bla.tmp">){if ($_ =~ /[^\t]+([,])[^\t]+[eE]/) {print "found forbidden symbol '$1' at $_ in $bla\n";&reset_locale();die;}}}
proteinortho-6.0.24+dfsg/proteinortho:2247: system("mv '$bla.tmp' '$bla'");
proteinortho-6.0.24+dfsg/proteinortho-2248-
##############################################
proteinortho-6.0.24+dfsg/proteinortho-2250-
proteinortho-6.0.24+dfsg/proteinortho:2251: system("$command");
proteinortho-6.0.24+dfsg/proteinortho-2252- if ($? != 0) {&Error($blastmode." failed with code $?.$NC (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)\nThe most common sources of this error are:\n- no space left on device error.\n- outdated $blastmode, please update $blastmode or consider another -p algorithm.\n- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'\n- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for $blastmode? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.");}
proteinortho-6.0.24+dfsg/proteinortho-2253- if($debug eq "test_sort"){while (<"$bla.tmp">){if ($_ =~ /[^\t]+([,])[^\t]+[eE]/) {print "found forbidden symbol '$1' at $_ in $bla\n";&reset_locale();die;}}}
proteinortho-6.0.24+dfsg/proteinortho:2254: system('awk -F\'\t\' \'{if($11<'.$evalue.')print $0}\' \''.$bla.'.tmp\' > \''.$bla.'\'');
proteinortho-6.0.24+dfsg/proteinortho-2255- unlink "$bla.tmp";
##############################################
proteinortho-6.0.24+dfsg/proteinortho-2258-
proteinortho-6.0.24+dfsg/proteinortho:2259: system("$command");
proteinortho-6.0.24+dfsg/proteinortho-2260- if ($? != 0) {&Error($blastmode." failed with code $?.$NC (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)\nThe most common sources of this error are:\n- no space left on device error.\n- outdated $blastmode, please update $blastmode or consider another -p algorithm.\n- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'\n- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for $blastmode? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.");}
proteinortho-6.0.24+dfsg/proteinortho:2261: system($binpath."mmseqs convertalis '$b.$blastmode' '$a.$blastmode' '$bla.tmp' '$bla.tmp2' >\/dev\/null 2>\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho-2262-
proteinortho-6.0.24+dfsg/proteinortho-2263- if($debug eq "test_sort"){while (<"$bla.tmp">){if ($_ =~ /[^\t]+([,])[^\t]+[eE]/) {print "found forbidden symbol '$1' at $_ in $bla.tmp\n";&reset_locale();die;}}}
proteinortho-6.0.24+dfsg/proteinortho:2264: system("rm '$bla'.*index*");
proteinortho-6.0.24+dfsg/proteinortho:2265: system('sed -re \'s/([0-9\.]+)(E)(\-|\+)([0-9\.]+)/\1e\3\4/g\' \''.$bla.'.tmp2\' >\''.$bla.'\' 2>\/dev\/null');
proteinortho-6.0.24+dfsg/proteinortho-2266- unlink "$bla.dbtype";
##############################################
proteinortho-6.0.24+dfsg/proteinortho-2272-
proteinortho-6.0.24+dfsg/proteinortho:2273: @data=`$command`;
proteinortho-6.0.24+dfsg/proteinortho-2274- if ($? != 0) {&Error($blastmode." failed with code $?.$NC (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)\nThe most common sources of this error are:\n- no space left on device error.\n- outdated $blastmode, please update $blastmode or consider another -p algorithm.\n- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'\n- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for $blastmode? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.");}
proteinortho-6.0.24+dfsg/proteinortho-2275- if($debug eq "test_sort"){while (<"$bla.tmp">){if ($_ =~ /[^\t]+([,])[^\t]+[eE]/) {print "found forbidden symbol '$1' at $_ in $bla.tmp\n";&reset_locale();die;}}}
proteinortho-6.0.24+dfsg/proteinortho:2276: if($keep){system("mv '$bla.tmp' '$bla'");}
proteinortho-6.0.24+dfsg/proteinortho-2277-
##############################################
proteinortho-6.0.24+dfsg/proteinortho-2717- print STDERR ("$ORANGE [WARNING]$NC Found empty line in $file, removing it with perl -lne.$NC");
proteinortho-6.0.24+dfsg/proteinortho:2718: system('perl -lne \'if($_ ne ""){print "$_";}\' '.$file.' >'.$file.'.tmp');
proteinortho-6.0.24+dfsg/proteinortho:2719: system('mv '.$file.'.tmp '.$file);
proteinortho-6.0.24+dfsg/proteinortho-2720- if($step==2){
##############################################
proteinortho-6.0.24+dfsg/proteinortho-2815- &reset_locale();
proteinortho-6.0.24+dfsg/proteinortho:2816: if (!$keep && $tmp_path =~ m/\/proteinortho_cache_[^\/]+\d*\/$/ && $step!=1 ){system("rm -r $tmp_path >/dev/null 2>&1");}
proteinortho-6.0.24+dfsg/proteinortho-2817- exit 1;
##############################################
proteinortho-6.0.24+dfsg/src/proteinortho2tree.pl-140-close(TMP);
proteinortho-6.0.24+dfsg/src/proteinortho2tree.pl:141:system("cat '$file.tmp.matrix2' >>'$file.tmp.matrix'");
proteinortho-6.0.24+dfsg/src/proteinortho2tree.pl-142-
##############################################
proteinortho-6.0.24+dfsg/src/proteinortho_do_mcl.pl-133-
proteinortho-6.0.24+dfsg/src/proteinortho_do_mcl.pl:134:system('mcl '.$tmpfilename.' --abc -te '.$cores.' -o '.$raw_mcl_output.' 2>/dev/null');
proteinortho-6.0.24+dfsg/src/proteinortho_do_mcl.pl-135-
##############################################
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-165-
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:166: $result=`grep -nH '\\b$query_split[0]\\b' $ARGV[$v] 2>/dev/null`;
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-167- $num_result=scalar split("\n",$result);
##############################################
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-176- $did_found_a_in_input=1;
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:177: if($step ne "none"){print `proteinortho_grab_proteins.pl -E '\\b$query_split[0]\\b' $ARGV[$v]`."\n";}
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-178- }elsif($num_result>1){
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-179- print STDERR "! ERROR ! found '".$query_split_noesc[0]."' multiple times in ".$ARGV[$v].". This seems dangerous, make sure there are no duplicates present in your fasta files ! \n";
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:180: if($step ne "none"){print `proteinortho_grab_proteins.pl -E '\\b$query_split[0]\\b' $ARGV[$v]`."\n";}
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-181- }
##############################################
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-184-
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:185: $result=`grep -nH '\\b$query_split[1]\\b' $ARGV[$v] 2>/dev/null`;
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-186- $num_result=scalar split("\n",$result);
##############################################
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-196- $did_found_b_in_input=1;
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:197: if($step ne "none"){print `proteinortho_grab_proteins.pl -E '\\b$query_split[1]\\b' $ARGV[$v]`."\n";}
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-198-
##############################################
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-200- print STDERR "! ERROR ! found '".$query_split_noesc[1]."' multiple times in ".$ARGV[$v].". This seems dangerous, make sure there are no duplicates present in your fasta files ! \n";
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:201: if($step ne "none"){print `proteinortho_grab_proteins.pl -E '\\b$query_split[1]\\b' $ARGV[$v]`."\n";}
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-202- }
##############################################
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-236-
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:237: $result=`grep -nH '\\b$query_split[0]\\b' proteinortho_cache_$project/*.vs.* 2>/dev/null`;
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-238- $num_a_all_blast_hits=scalar split("\n",$result);
##############################################
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-244-
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:245: $result=`grep -nH '\\b$query_split[1]\\b' proteinortho_cache_$project/*.vs.* 2>/dev/null`;
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-246- $num_b_all_blast_hits=scalar split("\n",$result);
##############################################
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-250-
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:251: $result=`grep -nHE '(\\b$query_split[0]\\b\\t\\b$query_split[1]\\b)|(\\b$query_split[1]\\b\\t\\b$query_split[0]\\b)' proteinortho_cache_$project/*.vs.* 2>/dev/null`;
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-252- $num_ab_all_blast_hits=scalar split("\n",$result);
##############################################
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-263-
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:264: $result=`grep -nH '\\b$query_split[0]\\b' *.vs.* 2>/dev/null`;
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-265- $num_a_all_blast_hits=scalar split("\n",$result);
##############################################
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-271-
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:272: $result=`grep -nH '\\b$query_split[1]\\b' *.vs.* 2>/dev/null`;
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-273- $num_b_all_blast_hits=scalar split("\n",$result);
##############################################
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-277-
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:278: $result=`grep -nHE '(\\b$query_split[0]\\b\\t\\b$query_split[1]\\b)|(\\b$query_split[1]\\b\\t\\b$query_split[0]\\b)' *.vs.* 2>/dev/null`;
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-279- $num_ab_all_blast_hits=scalar split("\n",$result);
##############################################
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-294-
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:295: $result=`grep -nH '\\b$query_split[0]\\b' $project.blast-graph 2>/dev/null`;
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-296- $num_a_aRBH_hits=scalar split("\n",$result);
##############################################
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-298- print STDERR "the query '".$query_split_noesc[0]."' got $num_a_aRBH_hits reciprocal hit(s).\n";
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:299: if($step ne "none"){$noheader=0;$last_isHeaderLine=0;$isHeaderLine=1;@spl_header=();@spl=();foreach(split("\n",`head -n2 $project.blast-graph |tail -n1| perl -lne 'chomp;s/#//g;print "# file\tline\t\$_"'`.$result)){processLine($_);}print "\n";}
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-300-
##############################################
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-302-
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:303: $result=`grep -nH '\\b$query_split[1]\\b' $project.blast-graph 2>/dev/null`;
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-304- $num_b_aRBH_hits=scalar split("\n",$result);
##############################################
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-306- print STDERR "the query '".$query_split_noesc[1]."' got $num_b_aRBH_hits reciprocal hit(s).\n";
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:307: if($step ne "none"){$noheader=0;$last_isHeaderLine=0;$isHeaderLine=1;@spl_header=();@spl=();foreach(split("\n",`head -n2 $project.blast-graph |tail -n1| perl -lne 'chomp;s/#//g;print "# file\tline\t\$_"'`.$result)){processLine($_);}print "\n";}
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-308-
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:309: $result=`grep -nHE '(\\b$query_split[0]\\b\\t\\b$query_split[1]\\b)|(\\b$query_split[1]\\b\\t\\b$query_split[0]\\b)' $project.blast-graph 2>/dev/null`;
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-310- $num_ab_aRBH_hits=scalar split("\n",$result);
##############################################
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-312- print STDERR "both queries '".$query_split_noesc[0]."' and '".$query_split_noesc[1]."' have $num_ab_aRBH_hits reciprocal hit(s) with each other.\n";
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:313: if($step ne "none"){$last_isHeaderLine=0;$isHeaderLine=1;@spl_header=();@spl=();foreach(split("\n",`head -n2 $project.blast-graph |tail -n1| perl -lne 'chomp;s/#//g;print "# file\tline\t\$_"'`.$result)){processLine($_);}print "\n";}
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-314- }
##############################################
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-338-
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:339: $result=`grep -nH '\\b$query_split[0]\\b' $project.proteinortho-graph 2>/dev/null`;
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-340- $num_a_cluster_hits=scalar split("\n",$result);
##############################################
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-342- print STDERR "the query '".$query_split_noesc[0]."' got $num_a_cluster_hits putative ortholog(s).\n";
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:343: if($step ne "none"){$result=`echo '# file\tline\t'|tr -d '\n'; head -n2 $project.proteinortho-graph| tail -n1 | sed 's/#//g'`.$result;$noheader=0;$last_isHeaderLine=0;$isHeaderLine=1;@spl_header=();@spl=();foreach(split("\n",$result)){processLine($_);}print "\n";}
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-344-
##############################################
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-346-
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:347: $result=`grep -nH '\\b$query_split[1]\\b' $project.proteinortho-graph 2>/dev/null`;
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-348- $num_b_cluster_hits=scalar split("\n",$result);
##############################################
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-350- print STDERR "the query '".$query_split_noesc[1]."' got $num_b_cluster_hits putative ortholog(s).\n";
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:351: if($step ne "none"){$result=`echo '# file\tline\t'|tr -d '\n'; head -n2 $project.proteinortho-graph| tail -n1 | sed 's/#//g'`.$result;$noheader=0;$last_isHeaderLine=0;$isHeaderLine=1;@spl_header=();@spl=();foreach(split("\n",$result)){processLine($_);}print "\n";}
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-352-
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:353: $result=`grep -nHE '(\\b$query_split[0]\\b\\t\\b$query_split[1]\\b)|(\\b$query_split[1]\\b\\t\\b$query_split[0]\\b)' $project.proteinortho-graph 2>/dev/null`;
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-354- $num_ab_cluster_hits=scalar split("\n",$result);
##############################################
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-357- print STDERR "both queries '".$query_split_noesc[0]."' and '".$query_split_noesc[1]."' are putative ortholog(s).\n";
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:358: if($step ne "none"){$result=`echo '# file\tline\t'|tr -d '\n'; head -n2 $project.proteinortho-graph| tail -n1 | sed 's/#//g'`.$result;$noheader=0;$last_isHeaderLine=0;$isHeaderLine=1;@spl_header=();@spl=();foreach(split("\n",$result)){processLine($_);}print "\n";}
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-359- }else{
##############################################
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-373-
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:374: $result=`grep -nH '\\b$query_split[0]\\b' $project.proteinortho.tsv 2>/dev/null`;
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-375- $num_a_cluster_groups=scalar split("\n",$result);
##############################################
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-377- print STDERR "the query '".$query_split_noesc[0]."' is part of $num_a_cluster_groups group(s) of putative orthologs.\n";
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:378: if($step ne "none"){$result=`head -n1 $project.proteinortho.tsv | perl -lne 'chomp;s/#//g;print "# file\tline\t\$_"'`.$result;$noheader=0;$last_isHeaderLine=0;$isHeaderLine=1;@spl_header=();@spl=();foreach(split("\n",$result)){processLine($_);}print "\n";}
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-379-
##############################################
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-381-
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:382: $result=`grep -nH '\\b$query_split[1]\\b' $project.proteinortho.tsv 2>/dev/null`;
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-383- $num_b_cluster_groups=scalar split("\n",$result);
##############################################
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-385- print STDERR "the query '".$query_split_noesc[1]."' is part of $num_b_cluster_groups group(s) of putative orthologs.\n";
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:386: if($step ne "none"){$result=`head -n1 $project.proteinortho.tsv | perl -lne 'chomp;s/#//g;print "# file\tline\t\$_"'`.$result;$noheader=0;$last_isHeaderLine=0;$isHeaderLine=1;@spl_header=();@spl=();foreach(split("\n",$result)){processLine($_);}print "\n";}
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-387-
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:388: $result=`grep -nHE '(\\b$query_split[0]\\b.*\\b$query_split[1]\\b)|(\\b$query_split[1]\\b.*\\b$query_split[0]\\b)' $project.proteinortho.tsv 2>/dev/null`;
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-389- $num_ab_cluster_groups=scalar split("\n",$result);
##############################################
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-391- print STDERR "both queries '".$query_split_noesc[0]."' and '".$query_split_noesc[1]."' have $num_ab_cluster_groups group(s) in common.\n";
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:392: if($step ne "none"){$result=`head -n1 $project.proteinortho.tsv | perl -lne 'chomp;s/#//g;print "# file\tline\t\$_"'`.$result;$noheader=0;$last_isHeaderLine=0;$isHeaderLine=1;@spl_header=();@spl=();foreach(split("\n",$result)){processLine($_);}print "\n";}
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-393-
##############################################
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-398-
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:399: $result=`grep -nH '\\b$query_split[0]\\b' $project.proteinortho 2>/dev/null`;
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-400- $num_a_cluster_groups=scalar split("\n",$result);
##############################################
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-402- print STDERR "the query '".$query_split_noesc[0]."' is part of $num_a_cluster_groups group(s) of putative orthologs.\n";
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:403: if($step ne "none"){$result=`head -n1 $project.proteinortho | perl -lne 'chomp;s/#//g;print "# file\tline\t\$_"'`.$result;$noheader=0;$last_isHeaderLine=0;$isHeaderLine=1;@spl_header=();@spl=();foreach(split("\n",$result)){processLine($_);}print "\n";}
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-404-
##############################################
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-406-
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:407: $result=`grep -nH '\\b$query_split[1]\\b' $project.proteinortho 2>/dev/null`;
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-408- $num_b_cluster_groups=scalar split("\n",$result);
##############################################
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-410- print STDERR "the query '".$query_split_noesc[1]."' is part of $num_b_cluster_groups group(s) of putative orthologs.\n";
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:411: if($step ne "none"){$result=`head -n1 $project.proteinortho | perl -lne 'chomp;s/#//g;print "# file\tline\t\$_"'`.$result;$noheader=0;$last_isHeaderLine=0;$isHeaderLine=1;@spl_header=();@spl=();foreach(split("\n",$result)){processLine($_);}print "\n";}
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-412-
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:413: $result=`grep -nHE '(\\b$query_split[0]\\b.*\\b$query_split[1]\\b)|(\\b$query_split[1]\\b.*\\b$query_split[0]\\b)' $project.proteinortho 2>/dev/null`;
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-414- $num_ab_cluster_groups=scalar split("\n",$result);
##############################################
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-416- print STDERR "both queries '".$query_split_noesc[0]."' and '".$query_split_noesc[1]."' have $num_ab_cluster_groups group(s) in common.\n";
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl:417: if($step ne "none"){$result=`head -n1 $project.proteinortho | perl -lne 'chomp;s/#//g;print "# file\tline\t\$_"'`.$result;$noheader=0;$last_isHeaderLine=0;$isHeaderLine=1;@spl_header=();@spl=();foreach(split("\n",$result)){processLine($_);}print "\n";}
proteinortho-6.0.24+dfsg/src/proteinortho_history.pl-418-
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-749- if(! -d $tmp_path."/proteinortho_cache_$project"){
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:750: system("mkdir $tmp_path/proteinortho_cache_$project");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-751- if( -d $tmp_path."/proteinortho_cache_$project"){
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-809- if($prefix eq $i_withoutEnd){
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:810: system("cp $files[$i] $tmp_path/".basename($files[$i])."; if [ ! -z \"\$(tail -c 1 \"$tmp_path/".basename($files[$i])."\")\" ]; then echo '' >> $tmp_path/".basename($files[$i])."; fi; cat ".$files[$j]." >>$tmp_path/".basename($files[$i]));
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-811- push(@new_files,"$tmp_path/".basename($files[$i]));
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-857- } else {
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:858: print STDERR "ps --forest -o pid,tty,stat,time,cmd -g $masterpid\n".`ps --forest -o pid,tty,stat,time,cmd -g $masterpid`."\n";
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-859- }
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-870- foreach my $file (keys %gene_counter) {
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:871: if($blastmode !~ m/blat/ && `ls '${file}'.${blastmode}* 1>/dev/null 2>&1` ne ""){ # test here
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-872- my $a = "$tmp_path/DB/".basename($file);
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:873: if(`ls '${a}'.${blastmode}* 1>/dev/null 2>&1` ne ""){ # or here
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-874- &Error("I did not find the database for ".$_[0]." (".$a."). Did you run --step=1 and maybe removed the databases? Please rerun 'proteinortho --step=1 --force /path/to/fastas' such that the databases can be recreated and then proceed with -step=2 and -step=3.");
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-894- if($synteny){
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:895: system("$po_path/proteinortho_cleanupblastgraph $syngraph"."* >tmp_$syngraph 2>/dev/null && mv tmp_$syngraph $syngraph"."_clean");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-896- $syngraph.="_clean";
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-898- }else{
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:899: system("$po_path/proteinortho_cleanupblastgraph $simgraph"."* >tmp_$simgraph 2>/dev/null && mv tmp_$simgraph $simgraph"."_clean");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-900- $simgraph.="_clean";
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-918-#clean up tmp dir
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:919:if (!$keep && $tmp_path =~ m/\/proteinortho_cache_[^\/]+\d*\/$/ && $step!=1){system("rm -r $tmp_path >/dev/null 2>&1");}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-920-
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-929- foreach my $file (@files) {
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:930: system("rm $file.$blastmode"."*");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-931- }
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-975- if($verbose == 2){ $cluster_verbose_level = "-debug 1 "; }
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:976: system ("OMP_PROC_BIND=$ompprocbind $po_path/proteinortho_clustering $cluster_verbose_level -minspecies $minspecies -ram ".$freemem_inMB." -kmere ".(1-$exactstep3)." -debug $debug -cpus $cpus -weighted 1 -conn $connectivity -purity $purity $clusterOptions -rmgraph '$rm_simgraph' $simgraph* >'$simtable'");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-977- if ($? != 0) {
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-980- }else{
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:981: my $stderrout = `$po_path/proteinortho_do_mcl.pl $cpus $simgraph*`;
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-982- if ($? != 0) {
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-985- }
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:986: system("mv mcl.proteinortho $simtable");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:987: system("mv mcl.proteinortho-graph $csimgraph");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-988- }
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-994-
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:995: system("(head -n 1 '$simtable' && tail -n +2 '$simtable' | sort -k1,2nr -k3,3gr ) > '$simtable.sort'; mv '$simtable.sort' '$simtable'");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-996-
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-999- my $fastas = "'".join("' '",@files)."'";
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1000: system("$po_path/proteinortho_singletons.pl $fastas <'$simtable' >>'$simtable'");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1001- }
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1004- if (!$nograph && !$useMcl) {
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1005: system("$po_path/proteinortho_graphMinusRemovegraph '$rm_simgraph' $simgraph* >'$csimgraph'");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1006- unless ($keep) {unlink($rm_simgraph);}
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1012- if(-x "$po_path/proteinortho_summary.pl"){
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1013: system("$po_path/proteinortho_summary.pl '$csimgraph' >>'$csimgraph.summary' 2>/dev/null");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1014- }
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1018- if(scalar @files < 10){
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1019: system("perl $po_path/proteinortho2html.pl $simtable '".join("' '",@files)."' >$simtablehtml");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1020- if($verbose){print STDERR "[OUTPUT] -> Orthologous groups are written to $simtablehtml\n";}
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1025- if ($doxml) {
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1026: system("perl $po_path/proteinortho2xml.pl $simtable >$simtable.xml");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1027: if ($? != 0) {system("rm $simtable.xml"); &Error("proteinortho2xml.pl failed");}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1028- if($verbose){print STDERR "[OUTPUT] -> Generated the ortho-xml file $simtable.xml";}
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1039- if($verbose == 2){ $cluster_verbose_level = "-debug 1 "; }
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1040: system ("OMP_PROC_BIND=$ompprocbind $po_path/proteinortho_clustering $cluster_verbose_level $clusterOptions -minspecies $minspecies -ram ".$freemem_inMB." -kmere ".(1-$exactstep3)." -debug $debug -cpus $cpus -weighted 1 -conn $connectivity -purity $purity $clusterOptions -rmgraph '$rm_syngraph' $syngraph* >'$syntable'");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1041- if ($? != 0) {
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1044- }else{
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1045: system($po_path.'/proteinortho_do_mcl.pl '.$cpus.' '.$syngraph.'*');
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1046: system("mv mcl.proteinortho $syntable");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1047: system("mv mcl.proteinortho-graph $csyngraph");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1048- }
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1049-
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1050: system("(head -n 1 '$syntable' && tail -n +2 '$syntable' | sort -k1,2nr -k3,3gr ) > '$syntable.sort'; mv '$syntable.sort' '$syntable'");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1051-
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1056- my $fastas = "'".join("' '",@files)."'";
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1057: system("$po_path/proteinortho_singletons.pl $fastas <'$syntable' >>'$syntable'");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1058- }
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1060- if (!$nograph && !$useMcl) {
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1061: system("$po_path/proteinortho_graphMinusRemovegraph '$rm_syngraph' $syngraph* >'$csyngraph'");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1062- unless ($keep) {unlink($rm_syngraph);}
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1067- if(-x "$po_path/proteinortho_summary.pl"){
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1068: system("$po_path/proteinortho_summary.pl '$csyngraph' >>'$csyngraph.summary'");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1069- }
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1071-
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1072: system("perl $po_path/proteinortho2html.pl $syntable '".join("' '",@files)."' >$syntablehtml");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1073- if($verbose){print STDERR "[OUTPUT] -> Orthologous groups are written to $syntablehtml\n";}
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1075- if ($doxml) {
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1076: system("perl $po_path/proteinortho2xml.pl $syntable >$syntable.xml");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1077: if ($? != 0) {system("rm $syntable.xml"); &Error("$ORANGE\n[WARNING]$NC -> proteinortho2xml.pl failed");}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1078- if($verbose){print STDERR "[OUTPUT] -> Generated the ortho-xml file $syntable.xml";}
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1444- print STDERR "\n$RED [Error] Failed to run $po_path/proteinortho_ffadj_mcs.py for\n$file_i vs $file_j\nMoving source to $temp_file.err for debugging\nI will continue, but results may be insufficient.$NC \n\n";
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1445: system("mv $temp_file.tmp $temp_file.err");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1446- next;
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1890-
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1891: if(!$force && `ls '${file}'.${blastmode}* 1>/dev/null 2>&1` ne ""){
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1892- if ($verbose) {print STDERR "The database for '$file' is present and will be used\n";}
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1894- if ($verbose) {print STDERR "Building database for '$file'\t(".$gene_counter{$file}." sequences)\n";}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1895: system("$makedb -d '$file' -n '$file.$blastmode' >\/dev\/null");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1896- if ($? != 0) {print STDERR ("$ORANGE\n[WARNING]$NC ".$blastmode." failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in $tmp_path (-tmp)."); if($step==1){print STDERR "$ORANGE Please ensure that you use -tmp=$tmp_path -keep (and use the same -project= name) for future analysis.$NC";}print "\n";
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1899- if($step==1){$oldkeep=$keep;$keep=1;}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1900: system("$makedb -d '$file' -n '$tmp_path/DB/".basename($file).".$blastmode' >\/dev\/null");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1901: system("ln -s '".abs_path($file)."' '$tmp_path/DB/".basename($file)."'");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1902-
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1911-
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1912: if(!$force && `ls '${file}'.${blastmode}* 1>/dev/null 2>&1` ne ""){
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1913- if ($verbose) {print STDERR "The database for '$file' is present and will be used\n";}
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1915- if ($verbose) {print STDERR "Building database for '$file'\t(".$gene_counter{$file}." sequences)\n";}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1916: system("$makedb '$file' -d '$file.$blastmode' --quiet >\/dev\/null 2>\/dev\/null");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1917- if ($? != 0) {print STDERR ("$ORANGE\n[WARNING]$NC ".$blastmode." failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in $tmp_path (-tmp)."); if($step==1){print STDERR "$ORANGE Please ensure that you use -tmp=$tmp_path -keep (and use the same -project= name) for future analysis.$NC";}print "\n";
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1920- if($step==1){$oldkeep=$keep;$keep=1;}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1921: system("$makedb '$file' -d '$tmp_path/DB/".basename($file).".$blastmode' --quiet >\/dev\/null 2>\/dev\/null");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1922: system("ln -s '".abs_path($file)."' '$tmp_path/DB/".basename($file)."'");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1923-
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1933-
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1934: if(!$force && `ls '${file}'.${blastmode}* 1>/dev/null 2>&1` ne ""){
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1935- if ($verbose) {print STDERR "The database for '$file' is present and will be used\n";}
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1937- if ($verbose) {print STDERR "Building database for '$file'\t(".$gene_counter{$file}." sequences)\n";}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1938: system("$makedb index -f '$file' -p '$file.$blastmode' >\/dev\/null 2>\/dev\/null");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1939- if ($? != 0) {print STDERR ("$ORANGE\n[WARNING]$NC ".$blastmode." failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in $tmp_path (-tmp)."); if($step==1){print STDERR "$ORANGE Please ensure that you use -tmp=$tmp_path -keep (and use the same -project= name) for future analysis.$NC";}print "\n";
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1942- if($step==1){$oldkeep=$keep;$keep=1;}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1943: system("$makedb index -f '$file' -p '$tmp_path/DB/".basename($file).".$blastmode' >\/dev\/null 2>\/dev\/null");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1944: system("ln -s '".abs_path($file)."' '$tmp_path/DB/".basename($file)."'");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1945-
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1954-
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1955: if(!$force && `ls '${file}'.${blastmode}* 1>/dev/null 2>&1` ne ""){
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1956- if ($verbose) {print STDERR "The database for '$file' is present and will be used\n";}
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1958- if ($verbose) {print STDERR "Building database for '$file'\t(".$gene_counter{$file}." sequences)\n";}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1959: system("$makedb --dbtype 1 '$file' '$file.$blastmode' >\/dev\/null 2>\/dev\/null");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1960- if ($? != 0) {print STDERR ("$ORANGE\n[WARNING]$NC ".$blastmode." failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in $tmp_path (-tmp)."); if($step==1){print STDERR "$ORANGE Please ensure that you use -tmp=$tmp_path -keep (and use the same -project= name) for future analysis.$NC";}print "\n";
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1963- if($step==1){$oldkeep=$keep;$keep=1;}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1964: system("$makedb --dbtype 1 '$file' '$tmp_path/DB/".basename($file).".$blastmode' >\/dev\/null 2>\/dev\/null");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1965: system("ln -s '".abs_path($file)."' '$tmp_path/DB/".basename($file)."'");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1966-
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1976-
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1977: if(!$force && `ls '${file}'.${blastmode}* 1>/dev/null 2>&1` ne ""){
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1978- if ($verbose) {print STDERR "The database for '$file' is present and will be used\n";}
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1980- if ($verbose) {print STDERR "Building database for '$file'\t(".$gene_counter{$file}." sequences)\n";}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1981: system("$makedb --dbtype 2 '$file' '$file.$blastmode' >\/dev\/null 2>\/dev\/null");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1982- if ($? != 0) {print STDERR ("$ORANGE\n[WARNING]$NC ".$blastmode." failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in $tmp_path (-tmp)."); if($step==1){print STDERR "$ORANGE Please ensure that you use -tmp=$tmp_path -keep (and use the same -project= name) for future analysis.$NC";}print "\n";
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1985- if($step==1){$oldkeep=$keep;$keep=1;}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1986: system("$makedb --dbtype 2 '$file' '$tmp_path/DB/".basename($file).".$blastmode' >\/dev\/null 2>\/dev\/null");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1987: system("ln -s '".abs_path($file)."' '$tmp_path/DB/".basename($file)."'");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1988-
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-1998-
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:1999: if(!$force && `ls '${file}'.${blastmode}* 1>/dev/null 2>&1` ne ""){
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2000- if ($verbose) {print STDERR "The database for '$file' is present and will be used\n";}
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2002- if ($verbose) {print STDERR "Building database for '$file'\t(".$gene_counter{$file}." sequences)\n";}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2003: system("$makedb '$file' -output '$file.$blastmode' >\/dev\/null 2>\/dev\/null");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2004- if ($? != 0) {print STDERR ("$ORANGE\n[WARNING]$NC ".$blastmode." failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in $tmp_path (-tmp)."); if($step==1){print STDERR "$ORANGE Please ensure that you use -tmp=$tmp_path -keep (and use the same -project= name) for future analysis.$NC";}print "\n";
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2007- if($step==1){$oldkeep=$keep;$keep=1;}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2008: system("$makedb '$file' -output '$tmp_path/DB/".basename($file).".$blastmode' >\/dev\/null 2>\/dev\/null");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2009: system("ln -s '".abs_path($file)."' '$tmp_path/DB/".basename($file)."'");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2010-
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2019-
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2020: if(!$force && `ls '${file}'.${blastmode}* 1>/dev/null 2>&1` ne ""){
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2021- if ($verbose) {print STDERR "The database for '$file' is present and will be used\n";}
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2024- if($blastmode eq "lastp"){
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2025: system("$makedb -p '$file.$blastmode' '$file'");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2026- if ($? != 0) {print STDERR ("$ORANGE\n[WARNING]$NC ".$blastmode." failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in $tmp_path (-tmp)."); if($step==1){print STDERR "$ORANGE Please ensure that you use -tmp=$tmp_path -keep (and use the same -project= name) for future analysis.$NC";}print "\n";
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2029- if($step==1){$oldkeep=$keep;$keep=1;}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2030: system("$makedb -p '$tmp_path/DB/".basename($file).".$blastmode' '$file'");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2031: system("ln -s '".abs_path($file)."' '$tmp_path/DB/".basename($file)."'");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2032-
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2035- }else{
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2036: system("$makedb '$file.$blastmode' '$file'");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2037- if ($? != 0) {print STDERR ("$ORANGE\n[WARNING]$NC ".$blastmode." failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in $tmp_path (-tmp)."); if($step==1){print STDERR "$ORANGE Please ensure that you use -tmp=$tmp_path -keep (and use the same -project= name) for future analysis.$NC";}print "\n";
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2040- if($step==1){$oldkeep=$keep;$keep=1;}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2041: system("$makedb '$tmp_path/DB/".basename($file).".$blastmode' '$file'");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2042: system("ln -s '".abs_path($file)."' '$tmp_path/DB/".basename($file)."'");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2043-
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2056-
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2057: if(!$force && `ls '${file}'.${blastmode}* 1>/dev/null 2>&1` ne ""){
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2058- if ($verbose) {print STDERR "The database for '$file' is present and will be used\n";}
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2061- if ($debug) {print STDERR "$makedb '$file' -out '$file.$blastmode' >\/dev\/null\n";}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2062: system("$makedb '$file' -out '$file.$blastmode' >\/dev\/null");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2063- if ($? != 0) {print STDERR ("$ORANGE\n[WARNING]$NC ".$blastmode." failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in $tmp_path (-tmp)."); if($step==1){print STDERR "$ORANGE Please ensure that you use -tmp=$tmp_path -keep (and use the same -project= name) for future analysis.$NC";}print "\n";
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2066- if($step==1){$oldkeep=$keep;$keep=1;}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2067: system("$makedb '$file' -out '$tmp_path/DB/".basename($file).".$blastmode' >\/dev\/null");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2068-
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2076-
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2077: if(!$force && `ls '${file}'.${blastmode}* 1>/dev/null 2>&1` ne ""){
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2078- if ($verbose) {print STDERR "The database for '$file' is present and will be used\n";}
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2085- if ($debug) {print STDERR "$makedb -dbtype ".$autoblast_fileis{$file}." -in '$file' -out '$file.$blastmode' >\/dev\/null\n";}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2086: system("$makedb -dbtype ".$autoblast_fileis{$file}." -in '$file' -out '$file.$blastmode' >\/dev\/null");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2087- if ($? != 0) {print STDERR ("$ORANGE\n[WARNING]$NC ".$blastmode." failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in $tmp_path (-tmp)."); if($step==1){print STDERR "$ORANGE Please ensure that you use -tmp=$tmp_path -keep (and use the same -project= name) for future analysis.$NC";}print "\n";
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2090- if($step==1){$oldkeep=$keep;$keep=1;}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2091: system("$makedb '$file' -out '$tmp_path/DB/".basename($file).".$blastmode' >\/dev\/null");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2092-
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2100-
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2101: if(!$force && `ls '${file}'.${blastmode}* 1>/dev/null 2>&1` ne ""){
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2102- if ($verbose) {print STDERR "The database for '$file' is present and will be used\n";}
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2105- if ($debug) {print STDERR "$makedb '$file' -out '$file.$blastmode' >\/dev\/null\n";}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2106: system("$makedb '$file' -n '$file.$blastmode' >\/dev\/null");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2107- if ($? != 0) {print STDERR ("$ORANGE\n[WARNING]$NC ".$blastmode." failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in $tmp_path (-tmp)."); if($step==1){print STDERR "$ORANGE Please ensure that you use -tmp=$tmp_path -keep (and use the same -project= name) for future analysis.$NC";}print "\n";
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2110- if($step==1){$oldkeep=$keep;$keep=1;}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2111: system("$makedb '$file' -n '$tmp_path/DB/".basename($file).".$blastmode' >\/dev\/null");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2112-
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2202- if ($blastmode eq "diamond") {
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2203: @data=`$command`; # run diamond
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2204- if ($? != 0) {&Error($blastmode." failed with code $?.$NC (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)\nThe most common sources of this error are:\n- no space left on device error.\n- outdated $blastmode, please update $blastmode or consider another -p algorithm.\n- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'\n- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for $blastmode? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.");}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2205- if($debug eq "test_sort"){while (<"$bla.tmp">){if ($_ =~ /[^\t]+([,])[^\t]+[eE]/) {print "found forbidden symbol '$1' at $_ in $bla\n";&reset_locale();die;}}}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2206: if($keep){system("mv '$bla.tmp' '$bla'");}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2207-
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2209-
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2210: system("$command");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2211- if ($? != 0) {&Error($blastmode." failed with code $?.$NC (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)\nThe most common sources of this error are:\n- no space left on device error.\n- outdated $blastmode, please update $blastmode or consider another -p algorithm.\n- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'\n- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for $blastmode? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.");}
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2217- unlink "$bla.aln"; #remove aln file
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2218: system("tail -n +6 '$bla.m82' >'$bla'"); # remove head/comment lines of rapsearch
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2219- unlink '$bla.m82';
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2223-
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2224: system("$command");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2225- if ($? != 0) {&Error($blastmode." failed with code $?.$NC (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)\nThe most common sources of this error are:\n- no space left on device error.\n- outdated $blastmode, please update $blastmode or consider another -p algorithm.\n- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'\n- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for $blastmode? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.");}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2226- if($debug eq "test_sort"){while (<"$bla.tmp">){if ($_ =~ /[^\t]+([,])[^\t]+[eE]/) {print "found forbidden symbol '$1' at $_ in $bla\n";&reset_locale();die;}}}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2227: system("perl $po_path/proteinortho_formatUsearch.pl '$bla.tmp' >'$bla'"); # problem with ublast/usearch: gene names include the description.
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2228- unlink "$bla.tmp";
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2231-
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2232: system("$command");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2233- if ($? != 0) {&Error($blastmode." failed with code $?.$NC (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)\nThe most common sources of this error are:\n- no space left on device error.\n- outdated $blastmode, please update $blastmode or consider another -p algorithm.\n- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'\n- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for $blastmode? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.");}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2234- if($debug eq "test_sort"){while (<"$bla.tmp">){if ($_ =~ /[^\t]+([,])[^\t]+[eE]/) {print "found forbidden symbol '$1' at $_ in $bla\n";&reset_locale();die;}}}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2235: system("tail -n +2 '$bla.tmp' > '$bla'");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2236- unlink "timing.txt";
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2240-
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2241: system("$command");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2242- if ($? != 0) {&Error($blastmode." failed with code $?.$NC (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)\nThe most common sources of this error are:\n- no space left on device error.\n- outdated $blastmode, please update $blastmode or consider another -p algorithm.\n- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'\n- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for $blastmode? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.");}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2243- if($debug eq "test_sort"){while (<"$bla.tmp">){if ($_ =~ /[^\t]+([,])[^\t]+[eE]/) {print "found forbidden symbol '$1' at $_ in $bla\n";&reset_locale();die;}}}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2244: system("mv '$bla.tmp' '$bla'");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2245-
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2247-
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2248: system("$command");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2249- if ($? != 0) {&Error($blastmode." failed with code $?.$NC (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)\nThe most common sources of this error are:\n- no space left on device error.\n- outdated $blastmode, please update $blastmode or consider another -p algorithm.\n- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'\n- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for $blastmode? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.");}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2250- if($debug eq "test_sort"){while (<"$bla.tmp">){if ($_ =~ /[^\t]+([,])[^\t]+[eE]/) {print "found forbidden symbol '$1' at $_ in $bla\n";&reset_locale();die;}}}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2251: system('awk -F\'\t\' \'{if($11<'.$evalue.')print $0}\' \''.$bla.'.tmp\' > \''.$bla.'\'');
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2252- unlink "$bla.tmp";
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2255-
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2256: system("$command");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2257- if ($? != 0) {&Error($blastmode." failed with code $?.$NC (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)\nThe most common sources of this error are:\n- no space left on device error.\n- outdated $blastmode, please update $blastmode or consider another -p algorithm.\n- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'\n- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for $blastmode? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.");}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2258: system($binpath."mmseqs convertalis '$b.$blastmode' '$a.$blastmode' '$bla.tmp' '$bla.tmp2' >\/dev\/null 2>\/dev\/null");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2259-
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2260- if($debug eq "test_sort"){while (<"$bla.tmp">){if ($_ =~ /[^\t]+([,])[^\t]+[eE]/) {print "found forbidden symbol '$1' at $_ in $bla.tmp\n";&reset_locale();die;}}}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2261: system("rm '$bla'.*index*");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2262: system('sed -re \'s/([0-9\.]+)(E)(\-|\+)([0-9\.]+)/\1e\3\4/g\' \''.$bla.'.tmp2\' >\''.$bla.'\' 2>\/dev\/null');
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2263- unlink "$bla.dbtype";
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2269-
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2270: @data=`$command`;
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2271- if ($? != 0) {&Error($blastmode." failed with code $?.$NC (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)\nThe most common sources of this error are:\n- no space left on device error.\n- outdated $blastmode, please update $blastmode or consider another -p algorithm.\n- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'\n- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for $blastmode? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.");}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2272- if($debug eq "test_sort"){while (<"$bla.tmp">){if ($_ =~ /[^\t]+([,])[^\t]+[eE]/) {print "found forbidden symbol '$1' at $_ in $bla.tmp\n";&reset_locale();die;}}}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2273: if($keep){system("mv '$bla.tmp' '$bla'");}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2274-
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2714- print STDERR ("$ORANGE [WARNING]$NC Found empty line in $file, removing it with perl -lne.$NC");
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2715: system('perl -lne \'if($_ ne ""){print "$_";}\' '.$file.' >'.$file.'.tmp');
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2716: system('mv '.$file.'.tmp '.$file);
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2717- if($step==2){
##############################################
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2812- &reset_locale();
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl:2813: if (!$keep && $tmp_path =~ m/\/proteinortho_cache_[^\/]+\d*\/$/ && $step!=1 ){system("rm -r $tmp_path >/dev/null 2>&1");}
proteinortho-6.0.24+dfsg/.pc/deb_diamond/proteinortho6.pl-2814- exit 1;
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-752- if(! -d $tmp_path."/proteinortho_cache_$project"){
proteinortho-6.0.24+dfsg/proteinortho6.pl:753: system("mkdir $tmp_path/proteinortho_cache_$project");
proteinortho-6.0.24+dfsg/proteinortho6.pl-754- if( -d $tmp_path."/proteinortho_cache_$project"){
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-812- if($prefix eq $i_withoutEnd){
proteinortho-6.0.24+dfsg/proteinortho6.pl:813: system("cp $files[$i] $tmp_path/".basename($files[$i])."; if [ ! -z \"\$(tail -c 1 \"$tmp_path/".basename($files[$i])."\")\" ]; then echo '' >> $tmp_path/".basename($files[$i])."; fi; cat ".$files[$j]." >>$tmp_path/".basename($files[$i]));
proteinortho-6.0.24+dfsg/proteinortho6.pl-814- push(@new_files,"$tmp_path/".basename($files[$i]));
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-860- } else {
proteinortho-6.0.24+dfsg/proteinortho6.pl:861: print STDERR "ps --forest -o pid,tty,stat,time,cmd -g $masterpid\n".`ps --forest -o pid,tty,stat,time,cmd -g $masterpid`."\n";
proteinortho-6.0.24+dfsg/proteinortho6.pl-862- }
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-873- foreach my $file (keys %gene_counter) {
proteinortho-6.0.24+dfsg/proteinortho6.pl:874: if($blastmode !~ m/blat/ && `ls '${file}'.${blastmode}* 1>/dev/null 2>&1` ne ""){ # test here
proteinortho-6.0.24+dfsg/proteinortho6.pl-875- my $a = "$tmp_path/DB/".basename($file);
proteinortho-6.0.24+dfsg/proteinortho6.pl:876: if(`ls '${a}'.${blastmode}* 1>/dev/null 2>&1` ne ""){ # or here
proteinortho-6.0.24+dfsg/proteinortho6.pl-877- &Error("I did not find the database for ".$_[0]." (".$a."). Did you run --step=1 and maybe removed the databases? Please rerun 'proteinortho --step=1 --force /path/to/fastas' such that the databases can be recreated and then proceed with -step=2 and -step=3.");
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-897- if($synteny){
proteinortho-6.0.24+dfsg/proteinortho6.pl:898: system("$po_path/proteinortho_cleanupblastgraph $syngraph"."* >tmp_$syngraph 2>/dev/null && mv tmp_$syngraph $syngraph"."_clean");
proteinortho-6.0.24+dfsg/proteinortho6.pl-899- $syngraph.="_clean";
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-901- }else{
proteinortho-6.0.24+dfsg/proteinortho6.pl:902: system("$po_path/proteinortho_cleanupblastgraph $simgraph"."* >tmp_$simgraph 2>/dev/null && mv tmp_$simgraph $simgraph"."_clean");
proteinortho-6.0.24+dfsg/proteinortho6.pl-903- $simgraph.="_clean";
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-921-#clean up tmp dir
proteinortho-6.0.24+dfsg/proteinortho6.pl:922:if (!$keep && $tmp_path =~ m/\/proteinortho_cache_[^\/]+\d*\/$/ && $step!=1){system("rm -r $tmp_path >/dev/null 2>&1");}
proteinortho-6.0.24+dfsg/proteinortho6.pl-923-
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-932- foreach my $file (@files) {
proteinortho-6.0.24+dfsg/proteinortho6.pl:933: system("rm $file.$blastmode"."*");
proteinortho-6.0.24+dfsg/proteinortho6.pl-934- }
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-978- if($verbose == 2){ $cluster_verbose_level = "-debug 1 "; }
proteinortho-6.0.24+dfsg/proteinortho6.pl:979: system ("OMP_PROC_BIND=$ompprocbind $po_path/proteinortho_clustering $cluster_verbose_level -minspecies $minspecies -ram ".$freemem_inMB." -kmere ".(1-$exactstep3)." -debug $debug -cpus $cpus -weighted 1 -conn $connectivity -purity $purity $clusterOptions -rmgraph '$rm_simgraph' $simgraph* >'$simtable'");
proteinortho-6.0.24+dfsg/proteinortho6.pl-980- if ($? != 0) {
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-983- }else{
proteinortho-6.0.24+dfsg/proteinortho6.pl:984: my $stderrout = `$po_path/proteinortho_do_mcl.pl $cpus $simgraph*`;
proteinortho-6.0.24+dfsg/proteinortho6.pl-985- if ($? != 0) {
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-988- }
proteinortho-6.0.24+dfsg/proteinortho6.pl:989: system("mv mcl.proteinortho $simtable");
proteinortho-6.0.24+dfsg/proteinortho6.pl:990: system("mv mcl.proteinortho-graph $csimgraph");
proteinortho-6.0.24+dfsg/proteinortho6.pl-991- }
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-997-
proteinortho-6.0.24+dfsg/proteinortho6.pl:998: system("(head -n 1 '$simtable' && tail -n +2 '$simtable' | sort -k1,2nr -k3,3gr ) > '$simtable.sort'; mv '$simtable.sort' '$simtable'");
proteinortho-6.0.24+dfsg/proteinortho6.pl-999-
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-1002- my $fastas = "'".join("' '",@files)."'";
proteinortho-6.0.24+dfsg/proteinortho6.pl:1003: system("$po_path/proteinortho_singletons.pl $fastas <'$simtable' >>'$simtable'");
proteinortho-6.0.24+dfsg/proteinortho6.pl-1004- }
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-1007- if (!$nograph && !$useMcl) {
proteinortho-6.0.24+dfsg/proteinortho6.pl:1008: system("$po_path/proteinortho_graphMinusRemovegraph '$rm_simgraph' $simgraph* >'$csimgraph'");
proteinortho-6.0.24+dfsg/proteinortho6.pl-1009- unless ($keep) {unlink($rm_simgraph);}
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-1015- if(-x "$po_path/proteinortho_summary.pl"){
proteinortho-6.0.24+dfsg/proteinortho6.pl:1016: system("$po_path/proteinortho_summary.pl '$csimgraph' >>'$csimgraph.summary' 2>/dev/null");
proteinortho-6.0.24+dfsg/proteinortho6.pl-1017- }
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-1021- if(scalar @files < 10){
proteinortho-6.0.24+dfsg/proteinortho6.pl:1022: system("perl $po_path/proteinortho2html.pl $simtable '".join("' '",@files)."' >$simtablehtml");
proteinortho-6.0.24+dfsg/proteinortho6.pl-1023- if($verbose){print STDERR "[OUTPUT] -> Orthologous groups are written to $simtablehtml\n";}
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-1028- if ($doxml) {
proteinortho-6.0.24+dfsg/proteinortho6.pl:1029: system("perl $po_path/proteinortho2xml.pl $simtable >$simtable.xml");
proteinortho-6.0.24+dfsg/proteinortho6.pl:1030: if ($? != 0) {system("rm $simtable.xml"); &Error("proteinortho2xml.pl failed");}
proteinortho-6.0.24+dfsg/proteinortho6.pl-1031- if($verbose){print STDERR "[OUTPUT] -> Generated the ortho-xml file $simtable.xml";}
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-1042- if($verbose == 2){ $cluster_verbose_level = "-debug 1 "; }
proteinortho-6.0.24+dfsg/proteinortho6.pl:1043: system ("OMP_PROC_BIND=$ompprocbind $po_path/proteinortho_clustering $cluster_verbose_level $clusterOptions -minspecies $minspecies -ram ".$freemem_inMB." -kmere ".(1-$exactstep3)." -debug $debug -cpus $cpus -weighted 1 -conn $connectivity -purity $purity $clusterOptions -rmgraph '$rm_syngraph' $syngraph* >'$syntable'");
proteinortho-6.0.24+dfsg/proteinortho6.pl-1044- if ($? != 0) {
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-1047- }else{
proteinortho-6.0.24+dfsg/proteinortho6.pl:1048: system($po_path.'/proteinortho_do_mcl.pl '.$cpus.' '.$syngraph.'*');
proteinortho-6.0.24+dfsg/proteinortho6.pl:1049: system("mv mcl.proteinortho $syntable");
proteinortho-6.0.24+dfsg/proteinortho6.pl:1050: system("mv mcl.proteinortho-graph $csyngraph");
proteinortho-6.0.24+dfsg/proteinortho6.pl-1051- }
proteinortho-6.0.24+dfsg/proteinortho6.pl-1052-
proteinortho-6.0.24+dfsg/proteinortho6.pl:1053: system("(head -n 1 '$syntable' && tail -n +2 '$syntable' | sort -k1,2nr -k3,3gr ) > '$syntable.sort'; mv '$syntable.sort' '$syntable'");
proteinortho-6.0.24+dfsg/proteinortho6.pl-1054-
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-1059- my $fastas = "'".join("' '",@files)."'";
proteinortho-6.0.24+dfsg/proteinortho6.pl:1060: system("$po_path/proteinortho_singletons.pl $fastas <'$syntable' >>'$syntable'");
proteinortho-6.0.24+dfsg/proteinortho6.pl-1061- }
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-1063- if (!$nograph && !$useMcl) {
proteinortho-6.0.24+dfsg/proteinortho6.pl:1064: system("$po_path/proteinortho_graphMinusRemovegraph '$rm_syngraph' $syngraph* >'$csyngraph'");
proteinortho-6.0.24+dfsg/proteinortho6.pl-1065- unless ($keep) {unlink($rm_syngraph);}
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-1070- if(-x "$po_path/proteinortho_summary.pl"){
proteinortho-6.0.24+dfsg/proteinortho6.pl:1071: system("$po_path/proteinortho_summary.pl '$csyngraph' >>'$csyngraph.summary'");
proteinortho-6.0.24+dfsg/proteinortho6.pl-1072- }
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-1074-
proteinortho-6.0.24+dfsg/proteinortho6.pl:1075: system("perl $po_path/proteinortho2html.pl $syntable '".join("' '",@files)."' >$syntablehtml");
proteinortho-6.0.24+dfsg/proteinortho6.pl-1076- if($verbose){print STDERR "[OUTPUT] -> Orthologous groups are written to $syntablehtml\n";}
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-1078- if ($doxml) {
proteinortho-6.0.24+dfsg/proteinortho6.pl:1079: system("perl $po_path/proteinortho2xml.pl $syntable >$syntable.xml");
proteinortho-6.0.24+dfsg/proteinortho6.pl:1080: if ($? != 0) {system("rm $syntable.xml"); &Error("$ORANGE\n[WARNING]$NC -> proteinortho2xml.pl failed");}
proteinortho-6.0.24+dfsg/proteinortho6.pl-1081- if($verbose){print STDERR "[OUTPUT] -> Generated the ortho-xml file $syntable.xml";}
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-1447- print STDERR "\n$RED [Error] Failed to run $po_path/proteinortho_ffadj_mcs.py for\n$file_i vs $file_j\nMoving source to $temp_file.err for debugging\nI will continue, but results may be insufficient.$NC \n\n";
proteinortho-6.0.24+dfsg/proteinortho6.pl:1448: system("mv $temp_file.tmp $temp_file.err");
proteinortho-6.0.24+dfsg/proteinortho6.pl-1449- next;
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-1893-
proteinortho-6.0.24+dfsg/proteinortho6.pl:1894: if(!$force && `ls '${file}'.${blastmode}* 1>/dev/null 2>&1` ne ""){
proteinortho-6.0.24+dfsg/proteinortho6.pl-1895- if ($verbose) {print STDERR "The database for '$file' is present and will be used\n";}
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-1897- if ($verbose) {print STDERR "Building database for '$file'\t(".$gene_counter{$file}." sequences)\n";}
proteinortho-6.0.24+dfsg/proteinortho6.pl:1898: system("$makedb -d '$file' -n '$file.$blastmode' >\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho6.pl-1899- if ($? != 0) {print STDERR ("$ORANGE\n[WARNING]$NC ".$blastmode." failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in $tmp_path (-tmp)."); if($step==1){print STDERR "$ORANGE Please ensure that you use -tmp=$tmp_path -keep (and use the same -project= name) for future analysis.$NC";}print "\n";
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-1902- if($step==1){$oldkeep=$keep;$keep=1;}
proteinortho-6.0.24+dfsg/proteinortho6.pl:1903: system("$makedb -d '$file' -n '$tmp_path/DB/".basename($file).".$blastmode' >\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho6.pl:1904: system("ln -s '".abs_path($file)."' '$tmp_path/DB/".basename($file)."'");
proteinortho-6.0.24+dfsg/proteinortho6.pl-1905-
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-1914-
proteinortho-6.0.24+dfsg/proteinortho6.pl:1915: if(!$force && `ls '${file}'.${blastmode}* 1>/dev/null 2>&1` ne ""){
proteinortho-6.0.24+dfsg/proteinortho6.pl-1916- if ($verbose) {print STDERR "The database for '$file' is present and will be used\n";}
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-1918- if ($verbose) {print STDERR "Building database for '$file'\t(".$gene_counter{$file}." sequences)\n";}
proteinortho-6.0.24+dfsg/proteinortho6.pl:1919: system("$makedb '$file' -d '$file.$blastmode' --quiet >\/dev\/null 2>\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho6.pl-1920- if ($? != 0) {print STDERR ("$ORANGE\n[WARNING]$NC ".$blastmode." failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in $tmp_path (-tmp)."); if($step==1){print STDERR "$ORANGE Please ensure that you use -tmp=$tmp_path -keep (and use the same -project= name) for future analysis.$NC";}print "\n";
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-1923- if($step==1){$oldkeep=$keep;$keep=1;}
proteinortho-6.0.24+dfsg/proteinortho6.pl:1924: system("$makedb '$file' -d '$tmp_path/DB/".basename($file).".$blastmode' --quiet >\/dev\/null 2>\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho6.pl:1925: system("ln -s '".abs_path($file)."' '$tmp_path/DB/".basename($file)."'");
proteinortho-6.0.24+dfsg/proteinortho6.pl-1926-
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-1936-
proteinortho-6.0.24+dfsg/proteinortho6.pl:1937: if(!$force && `ls '${file}'.${blastmode}* 1>/dev/null 2>&1` ne ""){
proteinortho-6.0.24+dfsg/proteinortho6.pl-1938- if ($verbose) {print STDERR "The database for '$file' is present and will be used\n";}
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-1940- if ($verbose) {print STDERR "Building database for '$file'\t(".$gene_counter{$file}." sequences)\n";}
proteinortho-6.0.24+dfsg/proteinortho6.pl:1941: system("$makedb index -f '$file' -p '$file.$blastmode' >\/dev\/null 2>\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho6.pl-1942- if ($? != 0) {print STDERR ("$ORANGE\n[WARNING]$NC ".$blastmode." failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in $tmp_path (-tmp)."); if($step==1){print STDERR "$ORANGE Please ensure that you use -tmp=$tmp_path -keep (and use the same -project= name) for future analysis.$NC";}print "\n";
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-1945- if($step==1){$oldkeep=$keep;$keep=1;}
proteinortho-6.0.24+dfsg/proteinortho6.pl:1946: system("$makedb index -f '$file' -p '$tmp_path/DB/".basename($file).".$blastmode' >\/dev\/null 2>\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho6.pl:1947: system("ln -s '".abs_path($file)."' '$tmp_path/DB/".basename($file)."'");
proteinortho-6.0.24+dfsg/proteinortho6.pl-1948-
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-1957-
proteinortho-6.0.24+dfsg/proteinortho6.pl:1958: if(!$force && `ls '${file}'.${blastmode}* 1>/dev/null 2>&1` ne ""){
proteinortho-6.0.24+dfsg/proteinortho6.pl-1959- if ($verbose) {print STDERR "The database for '$file' is present and will be used\n";}
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-1961- if ($verbose) {print STDERR "Building database for '$file'\t(".$gene_counter{$file}." sequences)\n";}
proteinortho-6.0.24+dfsg/proteinortho6.pl:1962: system("$makedb --dbtype 1 '$file' '$file.$blastmode' >\/dev\/null 2>\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho6.pl-1963- if ($? != 0) {print STDERR ("$ORANGE\n[WARNING]$NC ".$blastmode." failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in $tmp_path (-tmp)."); if($step==1){print STDERR "$ORANGE Please ensure that you use -tmp=$tmp_path -keep (and use the same -project= name) for future analysis.$NC";}print "\n";
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-1966- if($step==1){$oldkeep=$keep;$keep=1;}
proteinortho-6.0.24+dfsg/proteinortho6.pl:1967: system("$makedb --dbtype 1 '$file' '$tmp_path/DB/".basename($file).".$blastmode' >\/dev\/null 2>\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho6.pl:1968: system("ln -s '".abs_path($file)."' '$tmp_path/DB/".basename($file)."'");
proteinortho-6.0.24+dfsg/proteinortho6.pl-1969-
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-1979-
proteinortho-6.0.24+dfsg/proteinortho6.pl:1980: if(!$force && `ls '${file}'.${blastmode}* 1>/dev/null 2>&1` ne ""){
proteinortho-6.0.24+dfsg/proteinortho6.pl-1981- if ($verbose) {print STDERR "The database for '$file' is present and will be used\n";}
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-1983- if ($verbose) {print STDERR "Building database for '$file'\t(".$gene_counter{$file}." sequences)\n";}
proteinortho-6.0.24+dfsg/proteinortho6.pl:1984: system("$makedb --dbtype 2 '$file' '$file.$blastmode' >\/dev\/null 2>\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho6.pl-1985- if ($? != 0) {print STDERR ("$ORANGE\n[WARNING]$NC ".$blastmode." failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in $tmp_path (-tmp)."); if($step==1){print STDERR "$ORANGE Please ensure that you use -tmp=$tmp_path -keep (and use the same -project= name) for future analysis.$NC";}print "\n";
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-1988- if($step==1){$oldkeep=$keep;$keep=1;}
proteinortho-6.0.24+dfsg/proteinortho6.pl:1989: system("$makedb --dbtype 2 '$file' '$tmp_path/DB/".basename($file).".$blastmode' >\/dev\/null 2>\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho6.pl:1990: system("ln -s '".abs_path($file)."' '$tmp_path/DB/".basename($file)."'");
proteinortho-6.0.24+dfsg/proteinortho6.pl-1991-
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-2001-
proteinortho-6.0.24+dfsg/proteinortho6.pl:2002: if(!$force && `ls '${file}'.${blastmode}* 1>/dev/null 2>&1` ne ""){
proteinortho-6.0.24+dfsg/proteinortho6.pl-2003- if ($verbose) {print STDERR "The database for '$file' is present and will be used\n";}
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-2005- if ($verbose) {print STDERR "Building database for '$file'\t(".$gene_counter{$file}." sequences)\n";}
proteinortho-6.0.24+dfsg/proteinortho6.pl:2006: system("$makedb '$file' -output '$file.$blastmode' >\/dev\/null 2>\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho6.pl-2007- if ($? != 0) {print STDERR ("$ORANGE\n[WARNING]$NC ".$blastmode." failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in $tmp_path (-tmp)."); if($step==1){print STDERR "$ORANGE Please ensure that you use -tmp=$tmp_path -keep (and use the same -project= name) for future analysis.$NC";}print "\n";
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-2010- if($step==1){$oldkeep=$keep;$keep=1;}
proteinortho-6.0.24+dfsg/proteinortho6.pl:2011: system("$makedb '$file' -output '$tmp_path/DB/".basename($file).".$blastmode' >\/dev\/null 2>\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho6.pl:2012: system("ln -s '".abs_path($file)."' '$tmp_path/DB/".basename($file)."'");
proteinortho-6.0.24+dfsg/proteinortho6.pl-2013-
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-2022-
proteinortho-6.0.24+dfsg/proteinortho6.pl:2023: if(!$force && `ls '${file}'.${blastmode}* 1>/dev/null 2>&1` ne ""){
proteinortho-6.0.24+dfsg/proteinortho6.pl-2024- if ($verbose) {print STDERR "The database for '$file' is present and will be used\n";}
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-2027- if($blastmode eq "lastp"){
proteinortho-6.0.24+dfsg/proteinortho6.pl:2028: system("$makedb -p '$file.$blastmode' '$file'");
proteinortho-6.0.24+dfsg/proteinortho6.pl-2029- if ($? != 0) {print STDERR ("$ORANGE\n[WARNING]$NC ".$blastmode." failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in $tmp_path (-tmp)."); if($step==1){print STDERR "$ORANGE Please ensure that you use -tmp=$tmp_path -keep (and use the same -project= name) for future analysis.$NC";}print "\n";
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-2032- if($step==1){$oldkeep=$keep;$keep=1;}
proteinortho-6.0.24+dfsg/proteinortho6.pl:2033: system("$makedb -p '$tmp_path/DB/".basename($file).".$blastmode' '$file'");
proteinortho-6.0.24+dfsg/proteinortho6.pl:2034: system("ln -s '".abs_path($file)."' '$tmp_path/DB/".basename($file)."'");
proteinortho-6.0.24+dfsg/proteinortho6.pl-2035-
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-2038- }else{
proteinortho-6.0.24+dfsg/proteinortho6.pl:2039: system("$makedb '$file.$blastmode' '$file'");
proteinortho-6.0.24+dfsg/proteinortho6.pl-2040- if ($? != 0) {print STDERR ("$ORANGE\n[WARNING]$NC ".$blastmode." failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in $tmp_path (-tmp)."); if($step==1){print STDERR "$ORANGE Please ensure that you use -tmp=$tmp_path -keep (and use the same -project= name) for future analysis.$NC";}print "\n";
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-2043- if($step==1){$oldkeep=$keep;$keep=1;}
proteinortho-6.0.24+dfsg/proteinortho6.pl:2044: system("$makedb '$tmp_path/DB/".basename($file).".$blastmode' '$file'");
proteinortho-6.0.24+dfsg/proteinortho6.pl:2045: system("ln -s '".abs_path($file)."' '$tmp_path/DB/".basename($file)."'");
proteinortho-6.0.24+dfsg/proteinortho6.pl-2046-
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-2059-
proteinortho-6.0.24+dfsg/proteinortho6.pl:2060: if(!$force && `ls '${file}'.${blastmode}* 1>/dev/null 2>&1` ne ""){
proteinortho-6.0.24+dfsg/proteinortho6.pl-2061- if ($verbose) {print STDERR "The database for '$file' is present and will be used\n";}
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-2064- if ($debug) {print STDERR "$makedb '$file' -out '$file.$blastmode' >\/dev\/null\n";}
proteinortho-6.0.24+dfsg/proteinortho6.pl:2065: system("$makedb '$file' -out '$file.$blastmode' >\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho6.pl-2066- if ($? != 0) {print STDERR ("$ORANGE\n[WARNING]$NC ".$blastmode." failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in $tmp_path (-tmp)."); if($step==1){print STDERR "$ORANGE Please ensure that you use -tmp=$tmp_path -keep (and use the same -project= name) for future analysis.$NC";}print "\n";
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-2069- if($step==1){$oldkeep=$keep;$keep=1;}
proteinortho-6.0.24+dfsg/proteinortho6.pl:2070: system("$makedb '$file' -out '$tmp_path/DB/".basename($file).".$blastmode' >\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho6.pl-2071-
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-2079-
proteinortho-6.0.24+dfsg/proteinortho6.pl:2080: if(!$force && `ls '${file}'.${blastmode}* 1>/dev/null 2>&1` ne ""){
proteinortho-6.0.24+dfsg/proteinortho6.pl-2081- if ($verbose) {print STDERR "The database for '$file' is present and will be used\n";}
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-2088- if ($debug) {print STDERR "$makedb -dbtype ".$autoblast_fileis{$file}." -in '$file' -out '$file.$blastmode' >\/dev\/null\n";}
proteinortho-6.0.24+dfsg/proteinortho6.pl:2089: system("$makedb -dbtype ".$autoblast_fileis{$file}." -in '$file' -out '$file.$blastmode' >\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho6.pl-2090- if ($? != 0) {print STDERR ("$ORANGE\n[WARNING]$NC ".$blastmode." failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in $tmp_path (-tmp)."); if($step==1){print STDERR "$ORANGE Please ensure that you use -tmp=$tmp_path -keep (and use the same -project= name) for future analysis.$NC";}print "\n";
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-2093- if($step==1){$oldkeep=$keep;$keep=1;}
proteinortho-6.0.24+dfsg/proteinortho6.pl:2094: system("$makedb '$file' -out '$tmp_path/DB/".basename($file).".$blastmode' >\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho6.pl-2095-
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-2103-
proteinortho-6.0.24+dfsg/proteinortho6.pl:2104: if(!$force && `ls '${file}'.${blastmode}* 1>/dev/null 2>&1` ne ""){
proteinortho-6.0.24+dfsg/proteinortho6.pl-2105- if ($verbose) {print STDERR "The database for '$file' is present and will be used\n";}
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-2108- if ($debug) {print STDERR "$makedb '$file' -out '$file.$blastmode' >\/dev\/null\n";}
proteinortho-6.0.24+dfsg/proteinortho6.pl:2109: system("$makedb '$file' -n '$file.$blastmode' >\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho6.pl-2110- if ($? != 0) {print STDERR ("$ORANGE\n[WARNING]$NC ".$blastmode." failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in $tmp_path (-tmp)."); if($step==1){print STDERR "$ORANGE Please ensure that you use -tmp=$tmp_path -keep (and use the same -project= name) for future analysis.$NC";}print "\n";
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-2113- if($step==1){$oldkeep=$keep;$keep=1;}
proteinortho-6.0.24+dfsg/proteinortho6.pl:2114: system("$makedb '$file' -n '$tmp_path/DB/".basename($file).".$blastmode' >\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho6.pl-2115-
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-2205- if ($blastmode eq "diamond") {
proteinortho-6.0.24+dfsg/proteinortho6.pl:2206: @data=`$command`; # run diamond
proteinortho-6.0.24+dfsg/proteinortho6.pl-2207- if ($? != 0) {&Error($blastmode." failed with code $?.$NC (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)\nThe most common sources of this error are:\n- no space left on device error.\n- outdated $blastmode, please update $blastmode or consider another -p algorithm.\n- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'\n- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for $blastmode? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.");}
proteinortho-6.0.24+dfsg/proteinortho6.pl-2208- if($debug eq "test_sort"){while (<"$bla.tmp">){if ($_ =~ /[^\t]+([,])[^\t]+[eE]/) {print "found forbidden symbol '$1' at $_ in $bla\n";&reset_locale();die;}}}
proteinortho-6.0.24+dfsg/proteinortho6.pl:2209: if($keep){system("mv '$bla.tmp' '$bla'");}
proteinortho-6.0.24+dfsg/proteinortho6.pl-2210-
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-2212-
proteinortho-6.0.24+dfsg/proteinortho6.pl:2213: system("$command");
proteinortho-6.0.24+dfsg/proteinortho6.pl-2214- if ($? != 0) {&Error($blastmode." failed with code $?.$NC (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)\nThe most common sources of this error are:\n- no space left on device error.\n- outdated $blastmode, please update $blastmode or consider another -p algorithm.\n- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'\n- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for $blastmode? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.");}
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-2220- unlink "$bla.aln"; #remove aln file
proteinortho-6.0.24+dfsg/proteinortho6.pl:2221: system("tail -n +6 '$bla.m82' >'$bla'"); # remove head/comment lines of rapsearch
proteinortho-6.0.24+dfsg/proteinortho6.pl-2222- unlink '$bla.m82';
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-2226-
proteinortho-6.0.24+dfsg/proteinortho6.pl:2227: system("$command");
proteinortho-6.0.24+dfsg/proteinortho6.pl-2228- if ($? != 0) {&Error($blastmode." failed with code $?.$NC (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)\nThe most common sources of this error are:\n- no space left on device error.\n- outdated $blastmode, please update $blastmode or consider another -p algorithm.\n- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'\n- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for $blastmode? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.");}
proteinortho-6.0.24+dfsg/proteinortho6.pl-2229- if($debug eq "test_sort"){while (<"$bla.tmp">){if ($_ =~ /[^\t]+([,])[^\t]+[eE]/) {print "found forbidden symbol '$1' at $_ in $bla\n";&reset_locale();die;}}}
proteinortho-6.0.24+dfsg/proteinortho6.pl:2230: system("perl $po_path/proteinortho_formatUsearch.pl '$bla.tmp' >'$bla'"); # problem with ublast/usearch: gene names include the description.
proteinortho-6.0.24+dfsg/proteinortho6.pl-2231- unlink "$bla.tmp";
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-2234-
proteinortho-6.0.24+dfsg/proteinortho6.pl:2235: system("$command");
proteinortho-6.0.24+dfsg/proteinortho6.pl-2236- if ($? != 0) {&Error($blastmode." failed with code $?.$NC (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)\nThe most common sources of this error are:\n- no space left on device error.\n- outdated $blastmode, please update $blastmode or consider another -p algorithm.\n- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'\n- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for $blastmode? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.");}
proteinortho-6.0.24+dfsg/proteinortho6.pl-2237- if($debug eq "test_sort"){while (<"$bla.tmp">){if ($_ =~ /[^\t]+([,])[^\t]+[eE]/) {print "found forbidden symbol '$1' at $_ in $bla\n";&reset_locale();die;}}}
proteinortho-6.0.24+dfsg/proteinortho6.pl:2238: system("tail -n +2 '$bla.tmp' > '$bla'");
proteinortho-6.0.24+dfsg/proteinortho6.pl-2239- unlink "timing.txt";
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-2243-
proteinortho-6.0.24+dfsg/proteinortho6.pl:2244: system("$command");
proteinortho-6.0.24+dfsg/proteinortho6.pl-2245- if ($? != 0) {&Error($blastmode." failed with code $?.$NC (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)\nThe most common sources of this error are:\n- no space left on device error.\n- outdated $blastmode, please update $blastmode or consider another -p algorithm.\n- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'\n- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for $blastmode? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.");}
proteinortho-6.0.24+dfsg/proteinortho6.pl-2246- if($debug eq "test_sort"){while (<"$bla.tmp">){if ($_ =~ /[^\t]+([,])[^\t]+[eE]/) {print "found forbidden symbol '$1' at $_ in $bla\n";&reset_locale();die;}}}
proteinortho-6.0.24+dfsg/proteinortho6.pl:2247: system("mv '$bla.tmp' '$bla'");
proteinortho-6.0.24+dfsg/proteinortho6.pl-2248-
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-2250-
proteinortho-6.0.24+dfsg/proteinortho6.pl:2251: system("$command");
proteinortho-6.0.24+dfsg/proteinortho6.pl-2252- if ($? != 0) {&Error($blastmode." failed with code $?.$NC (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)\nThe most common sources of this error are:\n- no space left on device error.\n- outdated $blastmode, please update $blastmode or consider another -p algorithm.\n- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'\n- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for $blastmode? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.");}
proteinortho-6.0.24+dfsg/proteinortho6.pl-2253- if($debug eq "test_sort"){while (<"$bla.tmp">){if ($_ =~ /[^\t]+([,])[^\t]+[eE]/) {print "found forbidden symbol '$1' at $_ in $bla\n";&reset_locale();die;}}}
proteinortho-6.0.24+dfsg/proteinortho6.pl:2254: system('awk -F\'\t\' \'{if($11<'.$evalue.')print $0}\' \''.$bla.'.tmp\' > \''.$bla.'\'');
proteinortho-6.0.24+dfsg/proteinortho6.pl-2255- unlink "$bla.tmp";
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-2258-
proteinortho-6.0.24+dfsg/proteinortho6.pl:2259: system("$command");
proteinortho-6.0.24+dfsg/proteinortho6.pl-2260- if ($? != 0) {&Error($blastmode." failed with code $?.$NC (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)\nThe most common sources of this error are:\n- no space left on device error.\n- outdated $blastmode, please update $blastmode or consider another -p algorithm.\n- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'\n- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for $blastmode? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.");}
proteinortho-6.0.24+dfsg/proteinortho6.pl:2261: system($binpath."mmseqs convertalis '$b.$blastmode' '$a.$blastmode' '$bla.tmp' '$bla.tmp2' >\/dev\/null 2>\/dev\/null");
proteinortho-6.0.24+dfsg/proteinortho6.pl-2262-
proteinortho-6.0.24+dfsg/proteinortho6.pl-2263- if($debug eq "test_sort"){while (<"$bla.tmp">){if ($_ =~ /[^\t]+([,])[^\t]+[eE]/) {print "found forbidden symbol '$1' at $_ in $bla.tmp\n";&reset_locale();die;}}}
proteinortho-6.0.24+dfsg/proteinortho6.pl:2264: system("rm '$bla'.*index*");
proteinortho-6.0.24+dfsg/proteinortho6.pl:2265: system('sed -re \'s/([0-9\.]+)(E)(\-|\+)([0-9\.]+)/\1e\3\4/g\' \''.$bla.'.tmp2\' >\''.$bla.'\' 2>\/dev\/null');
proteinortho-6.0.24+dfsg/proteinortho6.pl-2266- unlink "$bla.dbtype";
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-2272-
proteinortho-6.0.24+dfsg/proteinortho6.pl:2273: @data=`$command`;
proteinortho-6.0.24+dfsg/proteinortho6.pl-2274- if ($? != 0) {&Error($blastmode." failed with code $?.$NC (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)\nThe most common sources of this error are:\n- no space left on device error.\n- outdated $blastmode, please update $blastmode or consider another -p algorithm.\n- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'\n- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for $blastmode? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.");}
proteinortho-6.0.24+dfsg/proteinortho6.pl-2275- if($debug eq "test_sort"){while (<"$bla.tmp">){if ($_ =~ /[^\t]+([,])[^\t]+[eE]/) {print "found forbidden symbol '$1' at $_ in $bla.tmp\n";&reset_locale();die;}}}
proteinortho-6.0.24+dfsg/proteinortho6.pl:2276: if($keep){system("mv '$bla.tmp' '$bla'");}
proteinortho-6.0.24+dfsg/proteinortho6.pl-2277-
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-2717- print STDERR ("$ORANGE [WARNING]$NC Found empty line in $file, removing it with perl -lne.$NC");
proteinortho-6.0.24+dfsg/proteinortho6.pl:2718: system('perl -lne \'if($_ ne ""){print "$_";}\' '.$file.' >'.$file.'.tmp');
proteinortho-6.0.24+dfsg/proteinortho6.pl:2719: system('mv '.$file.'.tmp '.$file);
proteinortho-6.0.24+dfsg/proteinortho6.pl-2720- if($step==2){
##############################################
proteinortho-6.0.24+dfsg/proteinortho6.pl-2815- &reset_locale();
proteinortho-6.0.24+dfsg/proteinortho6.pl:2816: if (!$keep && $tmp_path =~ m/\/proteinortho_cache_[^\/]+\d*\/$/ && $step!=1 ){system("rm -r $tmp_path >/dev/null 2>&1");}
proteinortho-6.0.24+dfsg/proteinortho6.pl-2817- exit 1;