===========================================================
.___ __ __
_________________ __ __ __| _/|__|/ |_
/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
sprai-0.9.9.23+dfsg1/ca_ikki_v5.pl-179- my $prefix=sprintf("c%02d.fin",$from+1);
sprai-0.9.9.23+dfsg1/ca_ikki_v5.pl:180: `ln -s $raw_fastq $out_dirs[$from+1]/$prefix.$suffix.fq`;
sprai-0.9.9.23+dfsg1/ca_ikki_v5.pl-181-}
##############################################
sprai-0.9.9.23+dfsg1/ca_ikki_v5.pl-189- }
sprai-0.9.9.23+dfsg1/ca_ikki_v5.pl:190: `$fastqToCA -libraryname foo -technology pacbio-corrected -reads $out_dirs[$i]/$prefix.$suffix.fq > $out_dirs[$i]/$prefix.$suffix.frg`;
sprai-0.9.9.23+dfsg1/ca_ikki_v5.pl-191-}
##############################################
sprai-0.9.9.23+dfsg1/ca_ikki_v5.pl-205- my $prefix=sprintf("c%02d.fin",$i);
sprai-0.9.9.23+dfsg1/ca_ikki_v5.pl:206: `$runCA stopAfter=unitigger -dir $out_dirs[$i] -p asm_$p2[$i] -s $spec $out_dirs[$i]/$prefix.$suffix.frg 2>> $out_dirs[$i]/do_$prefix.$suffix.$now.log`;
sprai-0.9.9.23+dfsg1/ca_ikki_v5.pl-207-}
##############################################
sprai-0.9.9.23+dfsg1/check_circularity.pl-42- print STDERR " We remove the entire directory and start from scratch.\n";
sprai-0.9.9.23+dfsg1/check_circularity.pl:43: `rm -rf "$temporary_directory_name"`;
sprai-0.9.9.23+dfsg1/check_circularity.pl-44- if($?) {
##############################################
sprai-0.9.9.23+dfsg1/check_circularity.pl-111- print STDERR "\$ $command_line\n" if($debug > 0);
sprai-0.9.9.23+dfsg1/check_circularity.pl:112: @results = `$command_line`;
sprai-0.9.9.23+dfsg1/check_circularity.pl-113- print @results if($debug > 0);
##############################################
sprai-0.9.9.23+dfsg1/check_redundancy.pl-31-print STDERR "\$ $command_line\n" if($debug > 0);
sprai-0.9.9.23+dfsg1/check_redundancy.pl:32:@results = `$command_line`;
sprai-0.9.9.23+dfsg1/check_redundancy.pl-33-print @results if($debug > 0);
##############################################
sprai-0.9.9.23+dfsg1/configure-28-#possible relative path
sprai-0.9.9.23+dfsg1/configure:29:WORKINGDIR=`dirname $0`
sprai-0.9.9.23+dfsg1/configure-30-cd $WORKINGDIR
##############################################
sprai-0.9.9.23+dfsg1/doc/_build/html/_sources/README.txt-71-If you specify ``--prefix=/some/dir/``, Sprai will be installed under ``/some/dir/bin/`` directory. Otherwise, it will be installed in ``/usr/local/bin``.
sprai-0.9.9.23+dfsg1/doc/_build/html/_sources/README.txt:72:If you do not have a root access, probably you want to add ``--prefix=$HOME/local`` or so.
sprai-0.9.9.23+dfsg1/doc/_build/html/_sources/README.txt-73-If you are creating RPM package, you would add ``--prefix=/usr``.
##############################################
sprai-0.9.9.23+dfsg1/debian/man/ezez4makefile_v4.1-52-See the sprai package documentation in /usr/share/doc/sprai,
sprai-0.9.9.23+dfsg1/debian/man/ezez4makefile_v4.1:53:especially the example ec and pbasm spec files in /usr/share/doc/sprai/examples
##############################################
sprai-0.9.9.23+dfsg1/debian/man/ezez4makefile_v4.pl.1-52-See the sprai package documentation in /usr/share/doc/sprai,
sprai-0.9.9.23+dfsg1/debian/man/ezez4makefile_v4.pl.1:53:especially the example ec and pbasm spec files in /usr/share/doc/sprai/examples
##############################################
sprai-0.9.9.23+dfsg1/debian/man/ezez4qsub_vx1.1-52-See the sprai package documentation in /usr/share/doc/sprai,
sprai-0.9.9.23+dfsg1/debian/man/ezez4qsub_vx1.1:53:especially the example ec and pbasm spec files in /usr/share/doc/sprai/examples
##############################################
sprai-0.9.9.23+dfsg1/debian/man/ezez4qsub_vx1.pl.1-52-See the sprai package documentation in /usr/share/doc/sprai,
sprai-0.9.9.23+dfsg1/debian/man/ezez4qsub_vx1.pl.1:53:especially the example ec and pbasm spec files in /usr/share/doc/sprai/examples
##############################################
sprai-0.9.9.23+dfsg1/debian/man/ezez_vx1.1-52-See the sprai package documentation in /usr/share/doc/sprai,
sprai-0.9.9.23+dfsg1/debian/man/ezez_vx1.1:53:especially the example ec and pbasm spec files in /usr/share/doc/sprai/examples
##############################################
sprai-0.9.9.23+dfsg1/debian/man/ezez_vx1.pl.1-52-See the sprai package documentation in /usr/share/doc/sprai,
sprai-0.9.9.23+dfsg1/debian/man/ezez_vx1.pl.1:53:especially the example ec and pbasm spec files in /usr/share/doc/sprai/examples
##############################################
sprai-0.9.9.23+dfsg1/debian/man/sprai.1-52-See the sprai package documentation in /usr/share/doc/sprai,
sprai-0.9.9.23+dfsg1/debian/man/sprai.1:53:especially the example ec and pbasm spec files in /usr/share/doc/sprai/examples
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4qsub_vx1.pl-340-if(!-d $scriptdir){
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4qsub_vx1.pl:341: `mkdir $scriptdir`;
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4qsub_vx1.pl-342-}
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4qsub_vx1.pl-1426- if(!$opt_dryrun && $index == $from){
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4qsub_vx1.pl:1427: `qsub $qsub_script`;
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4qsub_vx1.pl-1428- }
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4qsub_vx1.pl-1439-#else{
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4qsub_vx1.pl:1440:# `$ca_command`;
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4qsub_vx1.pl-1441-#}
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4qsub_vx1.pl-1474- $original_time_stamps{"$child"} = $c_fs[9];
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4qsub_vx1.pl:1475: `touch $child`;
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4qsub_vx1.pl-1476- last;
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4qsub_vx1.pl-1486- $original_time_stamps{"$child"} = $c_fs[9];
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4qsub_vx1.pl:1487: `touch $child`;
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4qsub_vx1.pl-1488- last;
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4qsub_vx1.pl-1496- if(!$f_do && $child =~ /\.dfq\.gz$/){
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4qsub_vx1.pl:1497: my $ret = system("gzip -d -c -t $child 2> /dev/null");
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4qsub_vx1.pl-1498- if($ret){
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4qsub_vx1.pl-1500- $f_do=1;
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4qsub_vx1.pl:1501: `touch $child`;
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4qsub_vx1.pl-1502- }
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl-322- $com1 = sprintf("$pipefail time cat $parent | $PG0 - | $dumbbell_filter - | $PG - --prefix $tmp_dir/db%02d | gzip -c -1 > $child.tmp && mv $child.tmp $child",$from);
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl:323: `$com1`;
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl-324- }
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl-345- }
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl:346: `$com2`;
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl-347- }
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl-406-
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl:407: `$com1 & $com2 & wait`;
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl-408- }
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl-481-
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl:482: `$command`;
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl-483- }
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl-514-
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl:515: `$command`;
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl-516- }
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl-524- if(-e $child){
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl:525: `rm $child`;
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl-526- }
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl-535- $command .= sprintf("cat $files >> $child.tmp && mv $child.tmp $child");
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl:536: `$command`;
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl-537- }
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl-569-
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl:570: `$com`;
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl-571-=pod
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl-612-
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl:613: `$com1 & $com2 & wait`;
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl-614-=cut
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl-645- if($f_do){
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl:646: `$ca_command_2`;
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl-647- }
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl-666- {
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl:667: `gzip -d -c $tmp_dir/c00_0000.dfq.gz | dfq2fq_v2.pl --orig_depth - | count_chars.pl - > $tmp_dir/tmp.count`;
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl-668- my $count=0;
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl-688- }
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl:689: `(gzip -d -c $result_dir/c01.fin.idfq.gz | $PG1 - -g $estimated_genome_size -q | fq2fa.pl - > $tmp_dir/c01.fin.longestXx.fa) `;
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl-690-
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl-693- $command .= "fa2fq.pl $tmp_dir/c01.fin.longestXx.fa | fq2idfq.pl - | fq2fa.pl - > $tmp_dir/d01.fin.longestXx.fa";
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl:694: `$command`;
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl-695- }
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl-701- $command2.= sprintf("partition_fa.pl $tmp_dir/d01.fin.longestXx.fa $partition -p $tmp_dir/d01");
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl:702: `$command1 & $command2 & wait`;
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl-703- }
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl-713- }
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl:714: `$command wait`;
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl-715- }
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl-739- $original_time_stamps{"$child"} = $c_fs[9];
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl:740: `touch $child`;
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl-741- last;
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl-751- $original_time_stamps{"$child"} = $c_fs[9];
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl:752: `touch $child`;
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez_vx1.pl-753- last;
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl-342- printf $mh "$outdir/$ps/9-terminator/$ps.scf.fasta: $outdir/$ps.frg\n";
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl:343: printf $mh "\t${rreq}$ca_path/runCA -dir $outdir/`basename \$< .frg` -p `basename \$< .frg` -s $spec \$< \n";
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl-344- }
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl-643-# $partition should be run as array job and accessed as $SGE_TASK_ID
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl:644:# STR0=`expr $SGE_TASK_ID - 1`
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl:645:# PART=`printf '%04d' $STR0`
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl:646: my $partgen = q(STR0=`expr $SGE_TASK_ID - 1`
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl:647:PART=`printf '%04d' $STR0`
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl-648-);
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl-667- if($submit){
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl:668: my $retv=`qsub -o log/idfqgz -e log/idfqgz $jf`;
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl-669- if($retv =~ /Your job (\d+)/){
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl-687- if($submit){
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl:688: my $retv=`qsub -o log/makeblastdb -e log/makeblastdb -hold_jid $idfqjobids[$libi] $jf`;
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl-689- if($retv =~ /Your job (\d+)/){
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl-709- my $depends = join(",",@jobids);
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl:710: my $retv=`qsub -o log/makeblastdb -e log/makeblastdb -hold_jid $depends $jf`;
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl-711- if($retv =~ /Your job (\d+)/){
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl-732- if($submit){
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl:733: my $retv=`qsub -o log/partition -e log/partition -hold_jid $idfqjobids[$libi] $jf`;
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl-734- if($retv =~ /Your job (\d+)/){
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl-765- if($submit){
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl:766: my $retv=`qsub -o log/blast -e log/blast -hold_jid $nalfjid,$ipjid $jf`;
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl-767- if($retv =~ /Your job-array (\d+)/){
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl-795- my $depend = $jobids[$libi];
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl:796: my $retv=`qsub -o log/part_ec -e log/part_ec -hold_jid_ad $depend $jf`;
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl-797- if($retv =~ /Your job-array (\d+)/){
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl-815- my $depend = $t_jid_lib[$libi];
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl:816: my $retv=`qsub -o log -e log -hold_jid $depend $jf`;
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl-817- if($retv =~ /Your job (\d+)/){
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl-841- my $depend = $jid_vv{$valid_voters};
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl:842: my $retv=`qsub -o log -e log -hold_jid $depend $jf`;
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl-843- if($retv =~ /Your job (\d+)/){
##############################################
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl-860- my $depend = $t_jid;
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl:861: my $retv=`qsub -o log -e log -hold_jid $depend $jf`;
sprai-0.9.9.23+dfsg1/.pc/libexec.patch/ezez4makefile_v4.pl-862- if($retv =~ /Your job (\d+)/){
##############################################
sprai-0.9.9.23+dfsg1/ezez4qsub_vx1.pl-340-if(!-d $scriptdir){
sprai-0.9.9.23+dfsg1/ezez4qsub_vx1.pl:341: `mkdir $scriptdir`;
sprai-0.9.9.23+dfsg1/ezez4qsub_vx1.pl-342-}
##############################################
sprai-0.9.9.23+dfsg1/ezez4qsub_vx1.pl-1426- if(!$opt_dryrun && $index == $from){
sprai-0.9.9.23+dfsg1/ezez4qsub_vx1.pl:1427: `qsub $qsub_script`;
sprai-0.9.9.23+dfsg1/ezez4qsub_vx1.pl-1428- }
##############################################
sprai-0.9.9.23+dfsg1/ezez4qsub_vx1.pl-1439-#else{
sprai-0.9.9.23+dfsg1/ezez4qsub_vx1.pl:1440:# `$ca_command`;
sprai-0.9.9.23+dfsg1/ezez4qsub_vx1.pl-1441-#}
##############################################
sprai-0.9.9.23+dfsg1/ezez4qsub_vx1.pl-1474- $original_time_stamps{"$child"} = $c_fs[9];
sprai-0.9.9.23+dfsg1/ezez4qsub_vx1.pl:1475: `touch $child`;
sprai-0.9.9.23+dfsg1/ezez4qsub_vx1.pl-1476- last;
##############################################
sprai-0.9.9.23+dfsg1/ezez4qsub_vx1.pl-1486- $original_time_stamps{"$child"} = $c_fs[9];
sprai-0.9.9.23+dfsg1/ezez4qsub_vx1.pl:1487: `touch $child`;
sprai-0.9.9.23+dfsg1/ezez4qsub_vx1.pl-1488- last;
##############################################
sprai-0.9.9.23+dfsg1/ezez4qsub_vx1.pl-1496- if(!$f_do && $child =~ /\.dfq\.gz$/){
sprai-0.9.9.23+dfsg1/ezez4qsub_vx1.pl:1497: my $ret = system("gzip -d -c -t $child 2> /dev/null");
sprai-0.9.9.23+dfsg1/ezez4qsub_vx1.pl-1498- if($ret){
##############################################
sprai-0.9.9.23+dfsg1/ezez4qsub_vx1.pl-1500- $f_do=1;
sprai-0.9.9.23+dfsg1/ezez4qsub_vx1.pl:1501: `touch $child`;
sprai-0.9.9.23+dfsg1/ezez4qsub_vx1.pl-1502- }
##############################################
sprai-0.9.9.23+dfsg1/ezez_vx1.pl-322- $com1 = sprintf("$pipefail time cat $parent | $PG0 - | $dumbbell_filter - | $PG - --prefix $tmp_dir/db%02d | gzip -c -1 > $child.tmp && mv $child.tmp $child",$from);
sprai-0.9.9.23+dfsg1/ezez_vx1.pl:323: `$com1`;
sprai-0.9.9.23+dfsg1/ezez_vx1.pl-324- }
##############################################
sprai-0.9.9.23+dfsg1/ezez_vx1.pl-345- }
sprai-0.9.9.23+dfsg1/ezez_vx1.pl:346: `$com2`;
sprai-0.9.9.23+dfsg1/ezez_vx1.pl-347- }
##############################################
sprai-0.9.9.23+dfsg1/ezez_vx1.pl-406-
sprai-0.9.9.23+dfsg1/ezez_vx1.pl:407: `$com1 & $com2 & wait`;
sprai-0.9.9.23+dfsg1/ezez_vx1.pl-408- }
##############################################
sprai-0.9.9.23+dfsg1/ezez_vx1.pl-481-
sprai-0.9.9.23+dfsg1/ezez_vx1.pl:482: `$command`;
sprai-0.9.9.23+dfsg1/ezez_vx1.pl-483- }
##############################################
sprai-0.9.9.23+dfsg1/ezez_vx1.pl-514-
sprai-0.9.9.23+dfsg1/ezez_vx1.pl:515: `$command`;
sprai-0.9.9.23+dfsg1/ezez_vx1.pl-516- }
##############################################
sprai-0.9.9.23+dfsg1/ezez_vx1.pl-524- if(-e $child){
sprai-0.9.9.23+dfsg1/ezez_vx1.pl:525: `rm $child`;
sprai-0.9.9.23+dfsg1/ezez_vx1.pl-526- }
##############################################
sprai-0.9.9.23+dfsg1/ezez_vx1.pl-535- $command .= sprintf("cat $files >> $child.tmp && mv $child.tmp $child");
sprai-0.9.9.23+dfsg1/ezez_vx1.pl:536: `$command`;
sprai-0.9.9.23+dfsg1/ezez_vx1.pl-537- }
##############################################
sprai-0.9.9.23+dfsg1/ezez_vx1.pl-569-
sprai-0.9.9.23+dfsg1/ezez_vx1.pl:570: `$com`;
sprai-0.9.9.23+dfsg1/ezez_vx1.pl-571-=pod
##############################################
sprai-0.9.9.23+dfsg1/ezez_vx1.pl-612-
sprai-0.9.9.23+dfsg1/ezez_vx1.pl:613: `$com1 & $com2 & wait`;
sprai-0.9.9.23+dfsg1/ezez_vx1.pl-614-=cut
##############################################
sprai-0.9.9.23+dfsg1/ezez_vx1.pl-645- if($f_do){
sprai-0.9.9.23+dfsg1/ezez_vx1.pl:646: `$ca_command_2`;
sprai-0.9.9.23+dfsg1/ezez_vx1.pl-647- }
##############################################
sprai-0.9.9.23+dfsg1/ezez_vx1.pl-666- {
sprai-0.9.9.23+dfsg1/ezez_vx1.pl:667: `gzip -d -c $tmp_dir/c00_0000.dfq.gz | dfq2fq_v2.pl --orig_depth - | count_chars.pl - > $tmp_dir/tmp.count`;
sprai-0.9.9.23+dfsg1/ezez_vx1.pl-668- my $count=0;
##############################################
sprai-0.9.9.23+dfsg1/ezez_vx1.pl-688- }
sprai-0.9.9.23+dfsg1/ezez_vx1.pl:689: `(gzip -d -c $result_dir/c01.fin.idfq.gz | $PG1 - -g $estimated_genome_size -q | fq2fa.pl - > $tmp_dir/c01.fin.longestXx.fa) `;
sprai-0.9.9.23+dfsg1/ezez_vx1.pl-690-
##############################################
sprai-0.9.9.23+dfsg1/ezez_vx1.pl-693- $command .= "fa2fq.pl $tmp_dir/c01.fin.longestXx.fa | fq2idfq.pl - | fq2fa.pl - > $tmp_dir/d01.fin.longestXx.fa";
sprai-0.9.9.23+dfsg1/ezez_vx1.pl:694: `$command`;
sprai-0.9.9.23+dfsg1/ezez_vx1.pl-695- }
##############################################
sprai-0.9.9.23+dfsg1/ezez_vx1.pl-701- $command2.= sprintf("partition_fa.pl $tmp_dir/d01.fin.longestXx.fa $partition -p $tmp_dir/d01");
sprai-0.9.9.23+dfsg1/ezez_vx1.pl:702: `$command1 & $command2 & wait`;
sprai-0.9.9.23+dfsg1/ezez_vx1.pl-703- }
##############################################
sprai-0.9.9.23+dfsg1/ezez_vx1.pl-713- }
sprai-0.9.9.23+dfsg1/ezez_vx1.pl:714: `$command wait`;
sprai-0.9.9.23+dfsg1/ezez_vx1.pl-715- }
##############################################
sprai-0.9.9.23+dfsg1/ezez_vx1.pl-739- $original_time_stamps{"$child"} = $c_fs[9];
sprai-0.9.9.23+dfsg1/ezez_vx1.pl:740: `touch $child`;
sprai-0.9.9.23+dfsg1/ezez_vx1.pl-741- last;
##############################################
sprai-0.9.9.23+dfsg1/ezez_vx1.pl-751- $original_time_stamps{"$child"} = $c_fs[9];
sprai-0.9.9.23+dfsg1/ezez_vx1.pl:752: `touch $child`;
sprai-0.9.9.23+dfsg1/ezez_vx1.pl-753- last;
##############################################
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl-342- printf $mh "$outdir/$ps/9-terminator/$ps.scf.fasta: $outdir/$ps.frg\n";
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl:343: printf $mh "\t${rreq}$ca_path/runCA -dir $outdir/`basename \$< .frg` -p `basename \$< .frg` -s $spec \$< \n";
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl-344- }
##############################################
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl-643-# $partition should be run as array job and accessed as $SGE_TASK_ID
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl:644:# STR0=`expr $SGE_TASK_ID - 1`
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl:645:# PART=`printf '%04d' $STR0`
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl:646: my $partgen = q(STR0=`expr $SGE_TASK_ID - 1`
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl:647:PART=`printf '%04d' $STR0`
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl-648-);
##############################################
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl-667- if($submit){
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl:668: my $retv=`qsub -o log/idfqgz -e log/idfqgz $jf`;
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl-669- if($retv =~ /Your job (\d+)/){
##############################################
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl-687- if($submit){
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl:688: my $retv=`qsub -o log/makeblastdb -e log/makeblastdb -hold_jid $idfqjobids[$libi] $jf`;
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl-689- if($retv =~ /Your job (\d+)/){
##############################################
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl-709- my $depends = join(",",@jobids);
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl:710: my $retv=`qsub -o log/makeblastdb -e log/makeblastdb -hold_jid $depends $jf`;
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl-711- if($retv =~ /Your job (\d+)/){
##############################################
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl-732- if($submit){
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl:733: my $retv=`qsub -o log/partition -e log/partition -hold_jid $idfqjobids[$libi] $jf`;
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl-734- if($retv =~ /Your job (\d+)/){
##############################################
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl-765- if($submit){
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl:766: my $retv=`qsub -o log/blast -e log/blast -hold_jid $nalfjid,$ipjid $jf`;
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl-767- if($retv =~ /Your job-array (\d+)/){
##############################################
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl-795- my $depend = $jobids[$libi];
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl:796: my $retv=`qsub -o log/part_ec -e log/part_ec -hold_jid_ad $depend $jf`;
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl-797- if($retv =~ /Your job-array (\d+)/){
##############################################
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl-815- my $depend = $t_jid_lib[$libi];
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl:816: my $retv=`qsub -o log -e log -hold_jid $depend $jf`;
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl-817- if($retv =~ /Your job (\d+)/){
##############################################
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl-841- my $depend = $jid_vv{$valid_voters};
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl:842: my $retv=`qsub -o log -e log -hold_jid $depend $jf`;
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl-843- if($retv =~ /Your job (\d+)/){
##############################################
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl-860- my $depend = $t_jid;
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl:861: my $retv=`qsub -o log -e log -hold_jid $depend $jf`;
sprai-0.9.9.23+dfsg1/ezez4makefile_v4.pl-862- if($retv =~ /Your job (\d+)/){