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/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
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grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
microbiomeutil-20101212+dfsg1/WigeoN/util/all_vs_all_WigeoN.pl-42-
microbiomeutil-20101212+dfsg1/WigeoN/util/all_vs_all_WigeoN.pl:43: my $ret = system($cmd);
microbiomeutil-20101212+dfsg1/WigeoN/util/all_vs_all_WigeoN.pl-44-
##############################################
microbiomeutil-20101212+dfsg1/WigeoN/PerlLib/CdbTools.pm-69-
microbiomeutil-20101212+dfsg1/WigeoN/PerlLib/CdbTools.pm:70: my $fastaEntry = `$cmd`;
microbiomeutil-20101212+dfsg1/WigeoN/PerlLib/CdbTools.pm-71- if ($?) {
##############################################
microbiomeutil-20101212+dfsg1/WigeoN/run_CM_to_WigeoN.pl-187-
microbiomeutil-20101212+dfsg1/WigeoN/run_CM_to_WigeoN.pl:188: my $result = `$cmd`;
microbiomeutil-20101212+dfsg1/WigeoN/run_CM_to_WigeoN.pl-189- if ($?) {
##############################################
microbiomeutil-20101212+dfsg1/WigeoN/run_CM_to_WigeoN.pl-224- my $cmd = "NAST-iEr $query_file.dbrenast.tmp $query_file.tmp > $query_file";
microbiomeutil-20101212+dfsg1/WigeoN/run_CM_to_WigeoN.pl:225: my $ret = system($cmd);
microbiomeutil-20101212+dfsg1/WigeoN/run_CM_to_WigeoN.pl-226-
##############################################
microbiomeutil-20101212+dfsg1/WigeoN/run_CM_to_WigeoN.pl-241- $cmd = "$FindBin::Bin/run_WigeoN.pl --query_NAST $query_file ";
microbiomeutil-20101212+dfsg1/WigeoN/run_CM_to_WigeoN.pl:242: my $ret = system($cmd);
microbiomeutil-20101212+dfsg1/WigeoN/run_CM_to_WigeoN.pl-243- if ($ret) {
##############################################
microbiomeutil-20101212+dfsg1/WigeoN/run_CM_to_WigeoN.pl-331-
microbiomeutil-20101212+dfsg1/WigeoN/run_CM_to_WigeoN.pl:332: my @results = `$cmd`;
microbiomeutil-20101212+dfsg1/WigeoN/run_CM_to_WigeoN.pl-333-
##############################################
microbiomeutil-20101212+dfsg1/WigeoN/run_WigeoN.pl-113- print STDERR "$cmd\n" if $VERBOSE;
microbiomeutil-20101212+dfsg1/WigeoN/run_WigeoN.pl:114: my $result = `$cmd`;
microbiomeutil-20101212+dfsg1/WigeoN/run_WigeoN.pl-115-
##############################################
microbiomeutil-20101212+dfsg1/WigeoN/run_WigeoN.pl-170- my $cmd = "formatdb -i $refDB -p F";
microbiomeutil-20101212+dfsg1/WigeoN/run_WigeoN.pl:171: system($cmd);
microbiomeutil-20101212+dfsg1/WigeoN/run_WigeoN.pl-172- }
##############################################
microbiomeutil-20101212+dfsg1/WigeoN/run_WigeoN.pl-187-
microbiomeutil-20101212+dfsg1/WigeoN/run_WigeoN.pl:188: my $result = `$cmd`;
microbiomeutil-20101212+dfsg1/WigeoN/run_WigeoN.pl-189- unlink($tmpfile);
##############################################
microbiomeutil-20101212+dfsg1/NAST-iEr/util/apply_NAST_MASK.pl-57-
microbiomeutil-20101212+dfsg1/NAST-iEr/util/apply_NAST_MASK.pl:58: my @x = `cat $file`;
microbiomeutil-20101212+dfsg1/NAST-iEr/util/apply_NAST_MASK.pl-59- shift @x; # rid header;
##############################################
microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data/testForUtils.pl-12-foreach my $prog (@progs) {
microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data/testForUtils.pl:13: my $path = `which $prog`;
microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data/testForUtils.pl-14- chomp $path;
##############################################
microbiomeutil-20101212+dfsg1/NAST-iEr/PerlLib/CdbTools.pm-69-
microbiomeutil-20101212+dfsg1/NAST-iEr/PerlLib/CdbTools.pm:70: my $fastaEntry = `$cmd`;
microbiomeutil-20101212+dfsg1/NAST-iEr/PerlLib/CdbTools.pm-71- if ($?) {
##############################################
microbiomeutil-20101212+dfsg1/NAST-iEr/iterative_refinement/quant_differences.pl-18-
microbiomeutil-20101212+dfsg1/NAST-iEr/iterative_refinement/quant_differences.pl:19: my $count_diff = `$cmd`;
microbiomeutil-20101212+dfsg1/NAST-iEr/iterative_refinement/quant_differences.pl-20- chomp $count_diff;
##############################################
microbiomeutil-20101212+dfsg1/NAST-iEr/iterative_refinement/iteratively_realign_db_selfsearch.pl-33-
microbiomeutil-20101212+dfsg1/NAST-iEr/iterative_refinement/iteratively_realign_db_selfsearch.pl:34: my $ret = system($cmd);
microbiomeutil-20101212+dfsg1/NAST-iEr/iterative_refinement/iteratively_realign_db_selfsearch.pl-35- if ($ret) {
##############################################
microbiomeutil-20101212+dfsg1/NAST-iEr/run_NAST-iEr.pl-98- my $cmd = "formatdb -i $db_FASTA -p F 2>/dev/null ";
microbiomeutil-20101212+dfsg1/NAST-iEr/run_NAST-iEr.pl:99: my $ret = system($cmd);
microbiomeutil-20101212+dfsg1/NAST-iEr/run_NAST-iEr.pl-100- if ($ret) {
##############################################
microbiomeutil-20101212+dfsg1/NAST-iEr/run_NAST-iEr.pl-126- #print "CMD: $cmd\n";
microbiomeutil-20101212+dfsg1/NAST-iEr/run_NAST-iEr.pl:127: my @hits = `$cmd`;
microbiomeutil-20101212+dfsg1/NAST-iEr/run_NAST-iEr.pl-128-
##############################################
microbiomeutil-20101212+dfsg1/ChimeraSlayer/PerlLib/CdbTools.pm-69-
microbiomeutil-20101212+dfsg1/ChimeraSlayer/PerlLib/CdbTools.pm:70: my $fastaEntry = `$cmd`;
microbiomeutil-20101212+dfsg1/ChimeraSlayer/PerlLib/CdbTools.pm-71- if ($?) {
##############################################
microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/run_chimeraParentSelector.pl-256-
microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/run_chimeraParentSelector.pl:257: my @results = `$cmd`;
microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/run_chimeraParentSelector.pl-258-
##############################################
microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/CPS_to_RENAST.pl-108- my $cmd = "$FindBin::Bin/../../NAST-iEr/NAST-iEr $query_file.dbrenast.tmp $query_file";
microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/CPS_to_RENAST.pl:109: my $renast = `$cmd`;
microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/CPS_to_RENAST.pl-110- my $ret = $?;
##############################################
microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraSlayer.pl-279- print "CMD: $cmd\n";
microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraSlayer.pl:280: my $ret = system($cmd);
microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraSlayer.pl-281-
##############################################
microbiomeutil-20101212+dfsg1/debian/tests/run-unit-test-4-if [ "$AUTOPKGTEST_TMP" = "" ] ; then
microbiomeutil-20101212+dfsg1/debian/tests/run-unit-test:5: AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
microbiomeutil-20101212+dfsg1/debian/tests/run-unit-test-6-fi
##############################################
microbiomeutil-20101212+dfsg1/.pc/find_relocated_resources.patch/ChimeraSlayer/ChimeraSlayer.pl-256- print "CMD: $cmd\n";
microbiomeutil-20101212+dfsg1/.pc/find_relocated_resources.patch/ChimeraSlayer/ChimeraSlayer.pl:257: my $ret = system($cmd);
microbiomeutil-20101212+dfsg1/.pc/find_relocated_resources.patch/ChimeraSlayer/ChimeraSlayer.pl-258-
##############################################
microbiomeutil-20101212+dfsg1/.pc/find_relocated_resources.patch/NAST-iEr/run_NAST-iEr.pl-76- my $cmd = "formatdb -i $db_FASTA -p F 2>/dev/null ";
microbiomeutil-20101212+dfsg1/.pc/find_relocated_resources.patch/NAST-iEr/run_NAST-iEr.pl:77: my $ret = system($cmd);
microbiomeutil-20101212+dfsg1/.pc/find_relocated_resources.patch/NAST-iEr/run_NAST-iEr.pl-78- if ($ret) {
##############################################
microbiomeutil-20101212+dfsg1/.pc/find_relocated_resources.patch/NAST-iEr/run_NAST-iEr.pl-104- #print "CMD: $cmd\n";
microbiomeutil-20101212+dfsg1/.pc/find_relocated_resources.patch/NAST-iEr/run_NAST-iEr.pl:105: my @hits = `$cmd`;
microbiomeutil-20101212+dfsg1/.pc/find_relocated_resources.patch/NAST-iEr/run_NAST-iEr.pl-106-
##############################################
microbiomeutil-20101212+dfsg1/.pc/find_relocated_resources.patch/WigeoN/run_WigeoN.pl-111- print STDERR "$cmd\n" if $VERBOSE;
microbiomeutil-20101212+dfsg1/.pc/find_relocated_resources.patch/WigeoN/run_WigeoN.pl:112: my $result = `$cmd`;
microbiomeutil-20101212+dfsg1/.pc/find_relocated_resources.patch/WigeoN/run_WigeoN.pl-113-
##############################################
microbiomeutil-20101212+dfsg1/.pc/find_relocated_resources.patch/WigeoN/run_WigeoN.pl-168- my $cmd = "formatdb -i $refDB -p F";
microbiomeutil-20101212+dfsg1/.pc/find_relocated_resources.patch/WigeoN/run_WigeoN.pl:169: system($cmd);
microbiomeutil-20101212+dfsg1/.pc/find_relocated_resources.patch/WigeoN/run_WigeoN.pl-170- }
##############################################
microbiomeutil-20101212+dfsg1/.pc/find_relocated_resources.patch/WigeoN/run_WigeoN.pl-185-
microbiomeutil-20101212+dfsg1/.pc/find_relocated_resources.patch/WigeoN/run_WigeoN.pl:186: my $result = `$cmd`;
microbiomeutil-20101212+dfsg1/.pc/find_relocated_resources.patch/WigeoN/run_WigeoN.pl-187- unlink($tmpfile);
##############################################
microbiomeutil-20101212+dfsg1/.pc/find_relocated_libraries.patch/ChimeraSlayer/ChimeraSlayer.pl-256- print "CMD: $cmd\n";
microbiomeutil-20101212+dfsg1/.pc/find_relocated_libraries.patch/ChimeraSlayer/ChimeraSlayer.pl:257: my $ret = system($cmd);
microbiomeutil-20101212+dfsg1/.pc/find_relocated_libraries.patch/ChimeraSlayer/ChimeraSlayer.pl-258-
##############################################
microbiomeutil-20101212+dfsg1/.pc/find_relocated_libraries.patch/NAST-iEr/run_NAST-iEr.pl-76- my $cmd = "formatdb -i $db_FASTA -p F 2>/dev/null ";
microbiomeutil-20101212+dfsg1/.pc/find_relocated_libraries.patch/NAST-iEr/run_NAST-iEr.pl:77: my $ret = system($cmd);
microbiomeutil-20101212+dfsg1/.pc/find_relocated_libraries.patch/NAST-iEr/run_NAST-iEr.pl-78- if ($ret) {
##############################################
microbiomeutil-20101212+dfsg1/.pc/find_relocated_libraries.patch/NAST-iEr/run_NAST-iEr.pl-104- #print "CMD: $cmd\n";
microbiomeutil-20101212+dfsg1/.pc/find_relocated_libraries.patch/NAST-iEr/run_NAST-iEr.pl:105: my @hits = `$cmd`;
microbiomeutil-20101212+dfsg1/.pc/find_relocated_libraries.patch/NAST-iEr/run_NAST-iEr.pl-106-
##############################################
microbiomeutil-20101212+dfsg1/.pc/find_relocated_libraries.patch/WigeoN/run_CM_to_WigeoN.pl-185-
microbiomeutil-20101212+dfsg1/.pc/find_relocated_libraries.patch/WigeoN/run_CM_to_WigeoN.pl:186: my $result = `$cmd`;
microbiomeutil-20101212+dfsg1/.pc/find_relocated_libraries.patch/WigeoN/run_CM_to_WigeoN.pl-187- if ($?) {
##############################################
microbiomeutil-20101212+dfsg1/.pc/find_relocated_libraries.patch/WigeoN/run_CM_to_WigeoN.pl-222- my $cmd = "NAST-iEr $query_file.dbrenast.tmp $query_file.tmp > $query_file";
microbiomeutil-20101212+dfsg1/.pc/find_relocated_libraries.patch/WigeoN/run_CM_to_WigeoN.pl:223: my $ret = system($cmd);
microbiomeutil-20101212+dfsg1/.pc/find_relocated_libraries.patch/WigeoN/run_CM_to_WigeoN.pl-224-
##############################################
microbiomeutil-20101212+dfsg1/.pc/find_relocated_libraries.patch/WigeoN/run_CM_to_WigeoN.pl-239- $cmd = "$FindBin::Bin/run_WigeoN.pl --query_NAST $query_file ";
microbiomeutil-20101212+dfsg1/.pc/find_relocated_libraries.patch/WigeoN/run_CM_to_WigeoN.pl:240: my $ret = system($cmd);
microbiomeutil-20101212+dfsg1/.pc/find_relocated_libraries.patch/WigeoN/run_CM_to_WigeoN.pl-241- if ($ret) {
##############################################
microbiomeutil-20101212+dfsg1/.pc/find_relocated_libraries.patch/WigeoN/run_CM_to_WigeoN.pl-329-
microbiomeutil-20101212+dfsg1/.pc/find_relocated_libraries.patch/WigeoN/run_CM_to_WigeoN.pl:330: my @results = `$cmd`;
microbiomeutil-20101212+dfsg1/.pc/find_relocated_libraries.patch/WigeoN/run_CM_to_WigeoN.pl-331-
##############################################
microbiomeutil-20101212+dfsg1/.pc/find_relocated_libraries.patch/WigeoN/run_WigeoN.pl-111- print STDERR "$cmd\n" if $VERBOSE;
microbiomeutil-20101212+dfsg1/.pc/find_relocated_libraries.patch/WigeoN/run_WigeoN.pl:112: my $result = `$cmd`;
microbiomeutil-20101212+dfsg1/.pc/find_relocated_libraries.patch/WigeoN/run_WigeoN.pl-113-
##############################################
microbiomeutil-20101212+dfsg1/.pc/find_relocated_libraries.patch/WigeoN/run_WigeoN.pl-168- my $cmd = "formatdb -i $refDB -p F";
microbiomeutil-20101212+dfsg1/.pc/find_relocated_libraries.patch/WigeoN/run_WigeoN.pl:169: system($cmd);
microbiomeutil-20101212+dfsg1/.pc/find_relocated_libraries.patch/WigeoN/run_WigeoN.pl-170- }
##############################################
microbiomeutil-20101212+dfsg1/.pc/find_relocated_libraries.patch/WigeoN/run_WigeoN.pl-185-
microbiomeutil-20101212+dfsg1/.pc/find_relocated_libraries.patch/WigeoN/run_WigeoN.pl:186: my $result = `$cmd`;
microbiomeutil-20101212+dfsg1/.pc/find_relocated_libraries.patch/WigeoN/run_WigeoN.pl-187- unlink($tmpfile);
##############################################
microbiomeutil-20101212+dfsg1/.pc/enable_tests_in_local_dir.patch/NAST-iEr/run_NAST-iEr.pl-78- my $cmd = "formatdb -i $db_FASTA -p F 2>/dev/null ";
microbiomeutil-20101212+dfsg1/.pc/enable_tests_in_local_dir.patch/NAST-iEr/run_NAST-iEr.pl:79: my $ret = system($cmd);
microbiomeutil-20101212+dfsg1/.pc/enable_tests_in_local_dir.patch/NAST-iEr/run_NAST-iEr.pl-80- if ($ret) {
##############################################
microbiomeutil-20101212+dfsg1/.pc/enable_tests_in_local_dir.patch/NAST-iEr/run_NAST-iEr.pl-106- #print "CMD: $cmd\n";
microbiomeutil-20101212+dfsg1/.pc/enable_tests_in_local_dir.patch/NAST-iEr/run_NAST-iEr.pl:107: my @hits = `$cmd`;
microbiomeutil-20101212+dfsg1/.pc/enable_tests_in_local_dir.patch/NAST-iEr/run_NAST-iEr.pl-108-
##############################################
microbiomeutil-20101212+dfsg1/.pc/enable_tests_in_local_dir.patch/ChimeraSlayer/ChimeraSlayer.pl-258- print "CMD: $cmd\n";
microbiomeutil-20101212+dfsg1/.pc/enable_tests_in_local_dir.patch/ChimeraSlayer/ChimeraSlayer.pl:259: my $ret = system($cmd);
microbiomeutil-20101212+dfsg1/.pc/enable_tests_in_local_dir.patch/ChimeraSlayer/ChimeraSlayer.pl-260-