=========================================================== .___ __ __ _________________ __ __ __| _/|__|/ |_ / ___\_` __ \__ \ | | \/ __ | | \\_ __\ / /_/ > | \// __ \| | / /_/ | | || | \___ /|__| (____ /____/\____ | |__||__| /_____/ \/ \/ 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-} ############################################## 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);