===========================================================
                                      .___ __  __   
          _________________  __ __  __| _/|__|/  |_ 
         / ___\_` __ \__  \ |  |  \/ __ | | \\_  __\
        / /_/  >  | \// __ \|  |  / /_/ | |  ||  |  
        \___  /|__|  (____  /____/\____ | |__||__|  
       /_____/            \/           \/           
              grep rough audit - static analysis tool
                  v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
cd-hit-4.8.1/clstr_sql_tbl.pl-122-  if(-e $tbl_file_tmp){
cd-hit-4.8.1/clstr_sql_tbl.pl:123:    system("cp $tbl_file_tmp $tbl_file");
cd-hit-4.8.1/clstr_sql_tbl.pl:124:    system("rm -f $tbl_file_tmp");
cd-hit-4.8.1/clstr_sql_tbl.pl-125-  }
##############################################
cd-hit-4.8.1/make_multi_seq.pl-23-
cd-hit-4.8.1/make_multi_seq.pl:24:if (not -e $out_dir) {my $cmd = `mkdir $out_dir`;}
cd-hit-4.8.1/make_multi_seq.pl-25-
##############################################
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl-150-
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl:151:  $cmd = `mkdir $bl_dir $seq_dir`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl-152-
##############################################
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl-382-    last unless (-e "$fout.out");    #removed from last call
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl:383:    if (not $bl_STDIN) { $cmd = `rm -f $fout`; }
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl:384:    $cmd = `rm -f $bl_dir/$i.out`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl-385-  }
##############################################
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl-411-
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl:412:  $cmd = `sh $tmp_sh_script >/dev/null 2>&1 &`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl-413-  return;
##############################################
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl-859-     $cmd_line = "$formatdb -in $tmp_db" if ($bl_plus);
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl:860:  my $cmd = `$cmd_line`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl-861-     
##############################################
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl-874-  my ($i, $j, $k);
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl:875:  $cmd = `rm -f $tmp_db`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl:876:  $cmd = `rm -f $tmp_db.p*`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl:877:  $cmd = `rm -f $tmp_db.n*`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl-878-
##############################################
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl-1042-          $wait_flag = 1;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl:1043:          $cmd = `qdel -f $qsub_id`; #### at this point, all running jobs are not necessary,
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl-1044-          print LOG "force delete un necessary job $qsub_id\n";
##############################################
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl-1058-    foreach $i (@files) {
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl:1059:      $cmd = `rm -f $seq_dir/$i`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl-1060-      print LOG "remove un necessary seq file $i\n"
##############################################
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl-1084-      my $t = "psi-cd-hit-$j";
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl:1085:      my $cmd = `qsub -N $t $remote_sh_script`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl-1086-      my $qsub_id = 0;
##############################################
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl-1092-  elsif ($exec_mode eq "local") {
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl:1093:    #my $cmd = `sh $remote_sh_script >/dev/null 2>&1 &`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl:1094:    my $cmd = `sh $remote_sh_script`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl-1095-  }
##############################################
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl-1110-  if ($sh_file) {
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl:1111:    $local_sh = `cat $sh_file`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl-1112-  }
##############################################
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl-1166-  next if (-e "$seq_dir/\$id.lock");
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl:1167:  \$cmd = `touch $seq_dir/\$id.lock`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl-1168-
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl-1169-  if ($bl_STDIN) {
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl:1170:    \$cmd = `$bl2 $opti $seq_dir/\$id | $script_name -J parse_blout $bl_dir/\$id -c $NR_clstr -ce $NR_clstre -aS $opt_aS -aL $opt_aL -G $g_iden -prog $blast_prog -bs 1`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl-1171-  }
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl-1172-  else {
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl:1173:    \$cmd = `$bl2 $opti $seq_dir/\$id $opto $bl_dir/\$id`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl:1174:    \$cmd =                         `$script_name -J parse_blout $bl_dir/\$id -c $NR_clstr -ce $NR_clstre -aS $opt_aS -aL $opt_aL -G $g_iden -prog $blast_prog -bs 0`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl-1175-  }
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl:1176:  \$cmd = `rm -f  $seq_dir/\$id`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl:1177:  \$cmd = `rm -f  $seq_dir/\$id.lock`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl-1178-}
##############################################
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl-1181-\$tt = \$tu + \$ts + \$cu + \$cs;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl:1182:\$cmd = `echo \$tt >> $seq_dir/host.\$host.cpu`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl-1183-
##############################################
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl-1185-  close(REPERL);
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl:1186:  my $cmd = `chmod 755 $remote_perl_script`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl-1187-
##############################################
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl-1197-    if (-e $out) {
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl:1198:      my $last = `tail -1 $out`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local-old.pl-1199-      chop($last);
##############################################
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-140-  }
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl:141:  my $bl_ver = `$blast_exe -version`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-142-  if ($bl_ver =~ /blast/) {
##############################################
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-163-
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl:164:  $cmd = `mkdir $bl_dir $blm_dir $seq_dir`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-165-
##############################################
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-441-    last unless (-e "$fout.out");    #removed from last call
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl:442:    if (not $bl_STDIN) { $cmd = `rm -f $fout`; }
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl:443:    $cmd = `rm -f $bl_dir/$i.out`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-444-  }
##############################################
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-470-
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl:471:  $cmd = `sh $tmp_sh_script >/dev/null 2>&1 &`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-472-  return;
##############################################
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1000-     $cmd_line = "$formatdb -in $tmp_db" if ($bl_plus);
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl:1001:  my $cmd = `$cmd_line`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1002-     
##############################################
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1015-  my ($i, $j, $k);
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl:1016:  $cmd = `rm -f $tmp_db`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl:1017:  $cmd = `rm -f $tmp_db.p*`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl:1018:  $cmd = `rm -f $tmp_db.n*`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1019-
##############################################
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1197-      my $t = "psi-cd-hit-$j";
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl:1198:      my $cmd = `qsub -N $t $remote_sh_script $j`; #### pass $j to qsub command
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1199-      my $qsub_id = 0;
##############################################
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1205-  elsif ($exec_mode eq "local") {
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl:1206:    #my $cmd = `sh $remote_sh_script >/dev/null 2>&1 &`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl:1207:    my $cmd = `sh $remote_sh_script`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1208-  }
##############################################
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1255-
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl:1256:    $cmd = `rm -f $blm_dir/$blf`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1257-    print LOG "parse and then rm $blm_dir/$blf\n";
##############################################
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1275-          $wait_flag = 1;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl:1276:          $cmd = `qdel -f $qsub_id`; #### at this point, all running jobs are not necessary,
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1277-          print LOG "force delete un necessary job $qsub_id\n";
##############################################
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1291-    foreach $i (@files) {
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl:1292:      $cmd = `rm -f $seq_dir/$i`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1293-      print LOG "remove un necessary seq file $i\n"
##############################################
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1317-      my $t = "psi-cd-hit-$j";
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl:1318:      my $cmd = `qsub -N $t $remote_sh_script`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1319-      my $qsub_id = 0;
##############################################
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1325-  elsif ($exec_mode eq "local") {
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl:1326:    #my $cmd = `sh $remote_sh_script >/dev/null 2>&1 &`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl:1327:    my $cmd = `sh $remote_sh_script`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1328-  }
##############################################
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1343-  if ($sh_file) {
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl:1344:    $local_sh = `cat $sh_file`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1345-  }
##############################################
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1401-  next if (-e "$seq_dir/\$id.lock");
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl:1402:  \$cmd = `touch $seq_dir/\$id.lock`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1403-
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1404-  if ($num_multi_seq) {
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl:1405:    \$cmd = `$bl2 $opti $seq_dir/\$id $opto $bl_dir/\$id`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl:1406:    \$cmd =                         `$script_name -J parse_blout_multi $bl_dir/\$id -c $NR_clstr -ce $NR_clstre -aS $opt_aS -aL $opt_aL -G $g_iden -prog $blast_prog -bs 0 >> $blm_dir/\$host.\$instance`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1407-  }
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1408-  elsif ($bl_STDIN) {
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl:1409:    \$cmd = `$bl2 $opti $seq_dir/\$id | $script_name -J parse_blout $bl_dir/\$id -c $NR_clstr -ce $NR_clstre -aS $opt_aS -aL $opt_aL -G $g_iden -prog $blast_prog -bs 1`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1410-  }
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1411-  else {
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl:1412:    \$cmd = `$bl2 $opti $seq_dir/\$id $opto $bl_dir/\$id`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl:1413:    \$cmd =                         `$script_name -J parse_blout $bl_dir/\$id -c $NR_clstr -ce $NR_clstre -aS $opt_aS -aL $opt_aL -G $g_iden -prog $blast_prog -bs 0`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1414-  }
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl:1415:  \$cmd = `rm -f  $seq_dir/\$id`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl:1416:  \$cmd = `rm -f  $seq_dir/\$id.lock`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1417-}
##############################################
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1420-\$tt = \$tu + \$ts + \$cu + \$cs;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl:1421:\$cmd = `echo \$tt >> $seq_dir/host.\$host.\$instance.cpu`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1422-
##############################################
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1424-  close(REPERL);
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl:1425:  my $cmd = `chmod 755 $remote_perl_script`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1426-
##############################################
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1436-    if (-e $out) {
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl:1437:      my $last = `tail -1 $out`;
cd-hit-4.8.1/psi-cd-hit/psi-cd-hit-local.pl-1438-      chop($last);
##############################################
cd-hit-4.8.1/usecases/Miseq-16S/16S-ref-db-PE-splice.pl-126-  print "running $cmd_line\n";
cd-hit-4.8.1/usecases/Miseq-16S/16S-ref-db-PE-splice.pl:127:  $cmd = `$cmd_line`;
cd-hit-4.8.1/usecases/Miseq-16S/16S-ref-db-PE-splice.pl-128-
##############################################
cd-hit-4.8.1/usecases/Miseq-16S/16S-ref-db-PE-splice.pl-325-  print "running $cmd_line\n";
cd-hit-4.8.1/usecases/Miseq-16S/16S-ref-db-PE-splice.pl:326:  $cmd = `$cmd_line`;
cd-hit-4.8.1/usecases/Miseq-16S/16S-ref-db-PE-splice.pl-327-
cd-hit-4.8.1/usecases/Miseq-16S/16S-ref-db-PE-splice.pl-328-  die "Can not run $cd_hit_est" unless (-e "$output_R1_tmp.clstr");
cd-hit-4.8.1/usecases/Miseq-16S/16S-ref-db-PE-splice.pl:329:  $cmd = `mv $output_R1_tmp $output_R1`;
cd-hit-4.8.1/usecases/Miseq-16S/16S-ref-db-PE-splice.pl:330:  $cmd = `mv $output_R2_tmp $output_R2`;
cd-hit-4.8.1/usecases/Miseq-16S/16S-ref-db-PE-splice.pl:331:  $cmd = `mv $output_R1_tmp.clstr $output.clstr`;
cd-hit-4.8.1/usecases/Miseq-16S/16S-ref-db-PE-splice.pl-332-
##############################################
cd-hit-4.8.1/usecases/Miseq-16S/16S-ref-db-PE-splice.pl-337-    print "running $cmd_line\n";
cd-hit-4.8.1/usecases/Miseq-16S/16S-ref-db-PE-splice.pl:338:    $cmd = `$cmd_line`;
cd-hit-4.8.1/usecases/Miseq-16S/16S-ref-db-PE-splice.pl-339-    die "Can not run $cd_hit_est" unless (-e "$output_S_tmp.clstr");
cd-hit-4.8.1/usecases/Miseq-16S/16S-ref-db-PE-splice.pl:340:    $cmd = `mv $output_S_tmp $output_S`;
cd-hit-4.8.1/usecases/Miseq-16S/16S-ref-db-PE-splice.pl:341:    $cmd = `mv $output_S_tmp.clstr $output_S.clstr`;
cd-hit-4.8.1/usecases/Miseq-16S/16S-ref-db-PE-splice.pl-342-  }
##############################################
cd-hit-4.8.1/usecases/Miseq-16S/16S-ref-db-PE-splice.pl-344-
cd-hit-4.8.1/usecases/Miseq-16S/16S-ref-db-PE-splice.pl:345:$cmd = `rm -f $session*`;
cd-hit-4.8.1/usecases/Miseq-16S/16S-ref-db-PE-splice.pl-346-
##############################################
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl-60-
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl:61:$cmd = `mkdir -p $log_dir`       unless (-e $log_dir);
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl:62:$cmd = `mkdir -p $sh_dir`        unless (-e $sh_dir);
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl:63:$cmd = `mkdir -p $sh_bundle_dir` unless (-e $sh_bundle_dir);
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl-64-open(LOG, ">> $log_file") || die "can not write to $log_file";
##############################################
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl-76-    $NGS_sample_data{$id} = [@data];
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl:77:    if (not (-e $id)) { $cmd = `mkdir $id`;}
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl-78-  }
##############################################
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl-86-    $NGS_sample_data{$id} = [@data];
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl:87:    if (not (-e $id)) { $cmd = `mkdir $id`;}
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl-88-  }
##############################################
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl-394-      for ($i=0; $i<$t_job->{"no_parallel"}; $i++) {
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl:395:        $cmd = `sh $t_sh_file >/dev/null 2>&1 &`;
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl-396-      }
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl:397:      $cmd = `touch $t_sh_pid`;
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl-398-      $t_sample_job->{'status'} = "submitted";
##############################################
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl-431-        my $t_stdout = "$t_sh_file.$i.stdout";
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl:432:        $cmd = `qsub $t_execution->{"command_name_opt"} $t_job_id $t_execution->{"command_err_opt"} $t_stderr $t_execution->{"command_out_opt"} $t_stdout $t_sh_file 2>$log_fileq`;
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl-433-        my $qsub_id = 0;
##############################################
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl-491-      for ($i=0; $i<$t_nodes_per_job; $i++) {
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl:492:        $cmd = `qsub $t_execution->{"command_name_opt"} $t_job_id $t_execution->{"command_err_opt"} $t_stderr $t_execution->{"command_out_opt"} $t_stdout $t_sh_bundle 2>$log_fileq`;
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl-493-        my $qsub_id = 0;
##############################################
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl-551-
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl:552:        $cmd = `qsub $t_execution->{"command_name_opt"} $t_job_id $t_execution->{"command_err_opt"} $t_stderr $t_execution->{"command_out_opt"} $t_stdout $t_sh_bundle 2>$log_fileq`;
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl-553-        my $qsub_id = 0;
##############################################
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl-662-  if ($exe_type eq "sh") {
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl:663:    $cmd = `ps -ef | grep "$t_sh_file" | grep -v grep`;
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl-664-    if ($cmd =~ /\w/) { # still running 
##############################################
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl-695-      elsif ($queue_system eq "SGE") {
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl:696:        $cmd = `qstat -j $i | grep job_number`;
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl-697-        if ($cmd =~ /$i/) {
##############################################
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl-702-      else {
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl:703:        $cmd = `qstat -r $i | grep $i`;
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl-704-        $j = (split(/\D/,$cmd))[0];
##############################################
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl-1028-        #### find the qsub ids to be deleted 
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl:1029:        my $qids = `cat $t_sh_pid`; $qids =~ s/\n/ /g; $qids =~ s/\s+/ /g;
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl-1030-        print TMPSH "qdel $qids\n";
##############################################
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl-1067-      my $f_cpu      = $t_sample_job->{'cpu_file'};
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl:1068:      my $t_start    = `cat $f_start`;    $t_start =~ s/\s//g; $min_start = $t_start if ($t_start < $min_start);
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl:1069:      my $t_end      = `cat $f_complete`; $t_end   =~ s/\s//g; $max_end   = $t_end   if ($t_end   > $max_end);
cd-hit-4.8.1/usecases/Miseq-16S/NG-Omics-WF.pl-1070-      my $t_wall     = int($t_end - $t_start);
##############################################
cd-hit-4.8.1/usecases/Miseq-16S/cd-hit-otu-miseq-PE.pl-27-my ($i, $j, $k, $str, $cmd, $ll);
cd-hit-4.8.1/usecases/Miseq-16S/cd-hit-otu-miseq-PE.pl:28:$cmd = `mkdir -p $dir`;
cd-hit-4.8.1/usecases/Miseq-16S/cd-hit-otu-miseq-PE.pl-29-open(LOG, "> $LOGf") || die "can not write to $LOGf";
##############################################
cd-hit-4.8.1/usecases/Miseq-16S/cd-hit-otu-miseq-PE.pl-72-################################################################################
cd-hit-4.8.1/usecases/Miseq-16S/cd-hit-otu-miseq-PE.pl:73:my $seq_n = `grep -c "^>" $input`; $seq_n =~ s/\D//g;
cd-hit-4.8.1/usecases/Miseq-16S/cd-hit-otu-miseq-PE.pl-74-my $cutoff = int($seq_n * $abs_cutoff);
##############################################
cd-hit-4.8.1/usecases/Miseq-16S/cd-hit-otu-miseq-PE.pl-196-  print STDERR "$str\n";
cd-hit-4.8.1/usecases/Miseq-16S/cd-hit-otu-miseq-PE.pl:197:  my $cmd = `$str` unless ($debug_mode);
cd-hit-4.8.1/usecases/Miseq-16S/cd-hit-otu-miseq-PE.pl-198-  return $cmd;
##############################################
cd-hit-4.8.1/usecases/Miseq-16S/cd-hit-otu-miseq-PE.pl-203-  my $clstr = shift;
cd-hit-4.8.1/usecases/Miseq-16S/cd-hit-otu-miseq-PE.pl:204:  my $n = `grep -c "^>" $clstr`;
cd-hit-4.8.1/usecases/Miseq-16S/cd-hit-otu-miseq-PE.pl-205-     $n =~ s/\s//g;
##############################################
cd-hit-4.8.1/usecases/Miseq-16S/cd-hit-otu-miseq-PE.pl-210-  my $clstr = shift;
cd-hit-4.8.1/usecases/Miseq-16S/cd-hit-otu-miseq-PE.pl:211:  my $n = `grep -cv "^>" $clstr`;
cd-hit-4.8.1/usecases/Miseq-16S/cd-hit-otu-miseq-PE.pl-212-     $n =~ s/\s//g;
##############################################
cd-hit-4.8.1/usecases/Miseq-16S/cd-hit-otu-miseq-PE.pl-217-  my $faa  = shift;
cd-hit-4.8.1/usecases/Miseq-16S/cd-hit-otu-miseq-PE.pl:218:  my $n = `grep -c "^>" $faa`;
cd-hit-4.8.1/usecases/Miseq-16S/cd-hit-otu-miseq-PE.pl-219-     $n =~ s/\s//g;
##############################################
cd-hit-4.8.1/usecases/Miseq-16S/pool_samples.pl-20-my ($i, $j, $k, $cmd);
cd-hit-4.8.1/usecases/Miseq-16S/pool_samples.pl:21:$cmd = `mkdir $output` unless (-e $output);
cd-hit-4.8.1/usecases/Miseq-16S/pool_samples.pl-22-
##############################################
cd-hit-4.8.1/usecases/Miseq-16S/pool_samples.pl-57-      print STDERR "cat $source >> $target\n";
cd-hit-4.8.1/usecases/Miseq-16S/pool_samples.pl:58:      $cmd = `cat $source >> $target`;
cd-hit-4.8.1/usecases/Miseq-16S/pool_samples.pl-59-    }
##############################################
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-2d-para.pl-113-else {
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-2d-para.pl:114:  $cmd = `mkdir $work_dir`;
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-2d-para.pl-115-  assign_commands();
##############################################
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-2d-para.pl-121-if ($command_status[0] eq "wait") {
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-2d-para.pl:122:  $cmd = `$commands[0]`;
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-2d-para.pl-123-  $command_status[0] = "done";
##############################################
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-2d-para.pl-132-if ($command_status[1] eq "wait") {
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-2d-para.pl:133:  $cmd = `$commands[1]`;
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-2d-para.pl-134-  $command_status[1] = "done";
##############################################
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-2d-para.pl-207-    open(TSH, "> $tsh") || die;
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-2d-para.pl:208:    $cmd = `date > $tlock`;
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-2d-para.pl-209-    print TSH <<EOD;
##############################################
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-2d-para.pl-217-    if ($local_cpu) {
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-2d-para.pl:218:      $cmd = `sh $tsh  >/dev/null 2>&1 &`;
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-2d-para.pl-219-      $command_status[$i] = "run";
##############################################
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-2d-para.pl-244-    else {
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-2d-para.pl:245:      $cmd = `ssh -xqf $thost 'cd $pwd; sh $tsh  >/dev/null 2>&1 &'`;
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-2d-para.pl-246-      $command_status[$i] = "run";
##############################################
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-2d-para.pl-281-      print  "$clstr_merge_exe $tclstrs >> $out_clstr\n";
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-2d-para.pl:282:      $cmd = `$clstr_merge_exe $tclstrs >> $out_clstr`;
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-2d-para.pl-283-    }
##############################################
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-2d-para.pl-285-      print  "cat $tclstrs >> $out_clstr";
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-2d-para.pl:286:      $cmd = `cat $tclstrs >> $out_clstr`;    
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-2d-para.pl-287-
##############################################
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-2d-para.pl-310-  sleep(10);
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-2d-para.pl:311:  $cmd = `mv $out_clstr_ren $out_clstr`;
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-2d-para.pl-312-
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-2d-para.pl-313-  my $reps = join(" ", @indb2_left);
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-2d-para.pl:314:  $cmd = `cat $reps > $out`;
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-2d-para.pl-315-}
##############################################
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-2d-para.pl-317-if (1) {
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-2d-para.pl:318:  $cmd = `grep CPU $work_dir/*log`;
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-2d-para.pl-319-  my @lls = split(/\n/, $cmd);
##############################################
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-para.pl-102-else {
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-para.pl:103:  $cmd = `mkdir $work_dir`;
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-para.pl-104-  assign_commands();
##############################################
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-para.pl-110-if ($command_status[0] eq "wait") {
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-para.pl:111:  $cmd = `$commands[0]`;
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-para.pl-112-  $command_status[0] = "done";
##############################################
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-para.pl-182-    open(TSH, "> $tsh") || die;
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-para.pl:183:    $cmd = `date > $tlock`;
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-para.pl-184-    print TSH <<EOD;
##############################################
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-para.pl-192-    if ($local_cpu) {
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-para.pl:193:      $cmd = `sh $tsh  >/dev/null 2>&1 &`;
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-para.pl-194-      $command_status[$i] = "run";
##############################################
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-para.pl-219-    else {
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-para.pl:220:      $cmd = `ssh -xqf $thost 'cd $pwd; sh $tsh  >/dev/null 2>&1 &'`;
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-para.pl-221-      $command_status[$i] = "run";
##############################################
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-para.pl-258-      print  "$clstr_merge_exe $master_clstr $tclstrs >> $out_clstr\n";
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-para.pl:259:      $cmd = `$clstr_merge_exe $master_clstr $tclstrs >> $out_clstr`;
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-para.pl-260-    }
##############################################
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-para.pl-262-      print  "cat $master_clstr >> $out_clstr";
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-para.pl:263:      $cmd = `cat $master_clstr >> $out_clstr`;    
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-para.pl-264-    }
##############################################
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-para.pl-286-  sleep(10);
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-para.pl:287:  $cmd = `mv $out_clstr_ren $out_clstr`;
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-para.pl-288-
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-para.pl-289-  my $reps = join(" ", @reps);
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-para.pl:290:  $cmd = `cat $reps > $out`;
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-para.pl-291-}
##############################################
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-para.pl-293-if (1) {
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-para.pl:294:  $cmd = `grep CPU $work_dir/*log`;
cd-hit-4.8.1/.pc/enable_help2man.patch/cd-hit-para.pl-295-  my @lls = split(/\n/, $cmd);
##############################################
cd-hit-4.8.1/cd-hit-2d-para.pl-113-else {
cd-hit-4.8.1/cd-hit-2d-para.pl:114:  $cmd = `mkdir $work_dir`;
cd-hit-4.8.1/cd-hit-2d-para.pl-115-  assign_commands();
##############################################
cd-hit-4.8.1/cd-hit-2d-para.pl-121-if ($command_status[0] eq "wait") {
cd-hit-4.8.1/cd-hit-2d-para.pl:122:  $cmd = `$commands[0]`;
cd-hit-4.8.1/cd-hit-2d-para.pl-123-  $command_status[0] = "done";
##############################################
cd-hit-4.8.1/cd-hit-2d-para.pl-132-if ($command_status[1] eq "wait") {
cd-hit-4.8.1/cd-hit-2d-para.pl:133:  $cmd = `$commands[1]`;
cd-hit-4.8.1/cd-hit-2d-para.pl-134-  $command_status[1] = "done";
##############################################
cd-hit-4.8.1/cd-hit-2d-para.pl-207-    open(TSH, "> $tsh") || die;
cd-hit-4.8.1/cd-hit-2d-para.pl:208:    $cmd = `date > $tlock`;
cd-hit-4.8.1/cd-hit-2d-para.pl-209-    print TSH <<EOD;
##############################################
cd-hit-4.8.1/cd-hit-2d-para.pl-217-    if ($local_cpu) {
cd-hit-4.8.1/cd-hit-2d-para.pl:218:      $cmd = `sh $tsh  >/dev/null 2>&1 &`;
cd-hit-4.8.1/cd-hit-2d-para.pl-219-      $command_status[$i] = "run";
##############################################
cd-hit-4.8.1/cd-hit-2d-para.pl-244-    else {
cd-hit-4.8.1/cd-hit-2d-para.pl:245:      $cmd = `ssh -xqf $thost 'cd $pwd; sh $tsh  >/dev/null 2>&1 &'`;
cd-hit-4.8.1/cd-hit-2d-para.pl-246-      $command_status[$i] = "run";
##############################################
cd-hit-4.8.1/cd-hit-2d-para.pl-281-      print  "$clstr_merge_exe $tclstrs >> $out_clstr\n";
cd-hit-4.8.1/cd-hit-2d-para.pl:282:      $cmd = `$clstr_merge_exe $tclstrs >> $out_clstr`;
cd-hit-4.8.1/cd-hit-2d-para.pl-283-    }
##############################################
cd-hit-4.8.1/cd-hit-2d-para.pl-285-      print  "cat $tclstrs >> $out_clstr";
cd-hit-4.8.1/cd-hit-2d-para.pl:286:      $cmd = `cat $tclstrs >> $out_clstr`;    
cd-hit-4.8.1/cd-hit-2d-para.pl-287-
##############################################
cd-hit-4.8.1/cd-hit-2d-para.pl-310-  sleep(10);
cd-hit-4.8.1/cd-hit-2d-para.pl:311:  $cmd = `mv $out_clstr_ren $out_clstr`;
cd-hit-4.8.1/cd-hit-2d-para.pl-312-
cd-hit-4.8.1/cd-hit-2d-para.pl-313-  my $reps = join(" ", @indb2_left);
cd-hit-4.8.1/cd-hit-2d-para.pl:314:  $cmd = `cat $reps > $out`;
cd-hit-4.8.1/cd-hit-2d-para.pl-315-}
##############################################
cd-hit-4.8.1/cd-hit-2d-para.pl-317-if (1) {
cd-hit-4.8.1/cd-hit-2d-para.pl:318:  $cmd = `grep CPU $work_dir/*log`;
cd-hit-4.8.1/cd-hit-2d-para.pl-319-  my @lls = split(/\n/, $cmd);
##############################################
cd-hit-4.8.1/cd-hit-para.pl-102-else {
cd-hit-4.8.1/cd-hit-para.pl:103:  $cmd = `mkdir $work_dir`;
cd-hit-4.8.1/cd-hit-para.pl-104-  assign_commands();
##############################################
cd-hit-4.8.1/cd-hit-para.pl-110-if ($command_status[0] eq "wait") {
cd-hit-4.8.1/cd-hit-para.pl:111:  $cmd = `$commands[0]`;
cd-hit-4.8.1/cd-hit-para.pl-112-  $command_status[0] = "done";
##############################################
cd-hit-4.8.1/cd-hit-para.pl-182-    open(TSH, "> $tsh") || die;
cd-hit-4.8.1/cd-hit-para.pl:183:    $cmd = `date > $tlock`;
cd-hit-4.8.1/cd-hit-para.pl-184-    print TSH <<EOD;
##############################################
cd-hit-4.8.1/cd-hit-para.pl-192-    if ($local_cpu) {
cd-hit-4.8.1/cd-hit-para.pl:193:      $cmd = `sh $tsh  >/dev/null 2>&1 &`;
cd-hit-4.8.1/cd-hit-para.pl-194-      $command_status[$i] = "run";
##############################################
cd-hit-4.8.1/cd-hit-para.pl-219-    else {
cd-hit-4.8.1/cd-hit-para.pl:220:      $cmd = `ssh -xqf $thost 'cd $pwd; sh $tsh  >/dev/null 2>&1 &'`;
cd-hit-4.8.1/cd-hit-para.pl-221-      $command_status[$i] = "run";
##############################################
cd-hit-4.8.1/cd-hit-para.pl-258-      print  "$clstr_merge_exe $master_clstr $tclstrs >> $out_clstr\n";
cd-hit-4.8.1/cd-hit-para.pl:259:      $cmd = `$clstr_merge_exe $master_clstr $tclstrs >> $out_clstr`;
cd-hit-4.8.1/cd-hit-para.pl-260-    }
##############################################
cd-hit-4.8.1/cd-hit-para.pl-262-      print  "cat $master_clstr >> $out_clstr";
cd-hit-4.8.1/cd-hit-para.pl:263:      $cmd = `cat $master_clstr >> $out_clstr`;    
cd-hit-4.8.1/cd-hit-para.pl-264-    }
##############################################
cd-hit-4.8.1/cd-hit-para.pl-286-  sleep(10);
cd-hit-4.8.1/cd-hit-para.pl:287:  $cmd = `mv $out_clstr_ren $out_clstr`;
cd-hit-4.8.1/cd-hit-para.pl-288-
cd-hit-4.8.1/cd-hit-para.pl-289-  my $reps = join(" ", @reps);
cd-hit-4.8.1/cd-hit-para.pl:290:  $cmd = `cat $reps > $out`;
cd-hit-4.8.1/cd-hit-para.pl-291-}
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cd-hit-4.8.1/cd-hit-para.pl-293-if (1) {
cd-hit-4.8.1/cd-hit-para.pl:294:  $cmd = `grep CPU $work_dir/*log`;
cd-hit-4.8.1/cd-hit-para.pl-295-  my @lls = split(/\n/, $cmd);