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/ /_/ > | \// __ \| | / /_/ | | || |
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grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
fastml-3.11/www/fastml/FastML_Wrapper.pl-534- {
fastml-3.11/www/fastml/FastML_Wrapper.pl:535: system ("gzip $FORM{outDir}$file");
fastml-3.11/www/fastml/FastML_Wrapper.pl-536- }
##############################################
fastml-3.11/www/fastml/FastML_Wrapper.pl-543- #Marginal reconstruction
fastml-3.11/www/fastml/FastML_Wrapper.pl:544: system ("cp $VARS{marginal_seq_chars_and_indel} $FORM{outDir}sequences_of_the_marginal_reconstruction_including_indels.fas");
fastml-3.11/www/fastml/FastML_Wrapper.pl:545: system ("zip -r $FORM{outDir}$VARS{All_Outputs_Zip} sequences_of_the_marginal_reconstruction_including_indels.fas; rm -f $FORM{outDir}sequences_of_the_marginal_reconstruction_including_indels.fas");
fastml-3.11/www/fastml/FastML_Wrapper.pl-546-
##############################################
fastml-3.11/www/fastml/FastML_Wrapper.pl-548- {
fastml-3.11/www/fastml/FastML_Wrapper.pl:549: system ("cp $VARS{marginal_prob_chars_and_parsimony_indels} $FORM{outDir}sequences_of_marginal_reconstruction_characters_and_parsimony_indels.fas");
fastml-3.11/www/fastml/FastML_Wrapper.pl:550: system ("zip -r $FORM{outDir}$VARS{All_Outputs_Zip} sequences_of_marginal_reconstruction_characters_and_parsimony_indels.fas; rm -f $FORM{outDir}sequences_of_marginal_reconstruction_characters_and_parsimony_indels.fas");
fastml-3.11/www/fastml/FastML_Wrapper.pl-551- }
fastml-3.11/www/fastml/FastML_Wrapper.pl-552-
fastml-3.11/www/fastml/FastML_Wrapper.pl:553: system ("cp $VARS{seq_marginal} $FORM{outDir}sequences_of_the_marginal_reconstruction_without_reconstruction_of_indels.fas");
fastml-3.11/www/fastml/FastML_Wrapper.pl:554: system ("zip -r $FORM{outDir}$VARS{All_Outputs_Zip} sequences_of_the_marginal_reconstruction_without_reconstruction_of_indels.fas; rm -f $FORM{outDir}sequences_of_the_marginal_reconstruction_without_reconstruction_of_indels.fas");
fastml-3.11/www/fastml/FastML_Wrapper.pl-555-
##############################################
fastml-3.11/www/fastml/FastML_Wrapper.pl-559- {
fastml-3.11/www/fastml/FastML_Wrapper.pl:560: system ("cp $VARS{marginal_prob_chars_and_indel} $FORM{outDir}Max_probabilities_of_marginal_reconstruction_with_indels.txt");
fastml-3.11/www/fastml/FastML_Wrapper.pl:561: system ("zip -r $FORM{outDir}$VARS{All_Outputs_Zip} Max_probabilities_of_marginal_reconstruction_with_indels.txt; rm -f $FORM{outDir}Max_probabilities_of_marginal_reconstruction_with_indels.txt");
fastml-3.11/www/fastml/FastML_Wrapper.pl-562- }
fastml-3.11/www/fastml/FastML_Wrapper.pl-563-
fastml-3.11/www/fastml/FastML_Wrapper.pl:564: system ("cp $VARS{prob_marginal} $FORM{outDir}probabilities_of_the_marginal_reconstruction_without_indels.txt");
fastml-3.11/www/fastml/FastML_Wrapper.pl:565: system ("zip -r $FORM{outDir}$VARS{All_Outputs_Zip} probabilities_of_the_marginal_reconstruction_without_indels.txt; rm -f $FORM{outDir}probabilities_of_the_marginal_reconstruction_without_indels.txt");
fastml-3.11/www/fastml/FastML_Wrapper.pl-566-
##############################################
fastml-3.11/www/fastml/FastML_Wrapper.pl-568- {
fastml-3.11/www/fastml/FastML_Wrapper.pl:569: system ("cp $VARS{marginal_indel_prob} $FORM{outDir}probabilities_of_the_marginal_reconstruction_for_indels.txt");
fastml-3.11/www/fastml/FastML_Wrapper.pl:570: system ("zip -r $FORM{outDir}$VARS{All_Outputs_Zip} probabilities_of_the_marginal_reconstruction_for_indels.txt; rm -f $FORM{outDir}probabilities_of_the_marginal_reconstruction_for_indels.txt");
fastml-3.11/www/fastml/FastML_Wrapper.pl-571- }
##############################################
fastml-3.11/www/fastml/FastML_Wrapper.pl-575- {
fastml-3.11/www/fastml/FastML_Wrapper.pl:576: system ("cp $VARS{seq_joint} $FORM{outDir}sequences_of_the_joint_reconstruction.fas");
fastml-3.11/www/fastml/FastML_Wrapper.pl:577: system ("zip -r $FORM{outDir}$VARS{All_Outputs_Zip} sequences_of_the_joint_reconstruction.fas; rm -f $FORM{outDir}sequences_of_the_joint_reconstruction.fas");
fastml-3.11/www/fastml/FastML_Wrapper.pl-578-
fastml-3.11/www/fastml/FastML_Wrapper.pl:579: system ("cp $VARS{prob_joint} $FORM{outDir}probabilities_of_the_joint_reconstruction.txt");
fastml-3.11/www/fastml/FastML_Wrapper.pl:580: system ("zip -r $FORM{outDir}$VARS{All_Outputs_Zip} probabilities_of_the_joint_reconstruction.txt; rm -f $FORM{outDir}probabilities_of_the_joint_reconstruction.fas");
fastml-3.11/www/fastml/FastML_Wrapper.pl-581- }
##############################################
fastml-3.11/www/fastml/FastML_Wrapper.pl-583- #Phylogenetic tree
fastml-3.11/www/fastml/FastML_Wrapper.pl:584: system ("cp $VARS{tree_newick} $FORM{outDir}Tree.txt");
fastml-3.11/www/fastml/FastML_Wrapper.pl:585: system ("zip -r $FORM{outDir}$VARS{All_Outputs_Zip} Tree.txt; rm -f $FORM{outDir}Tree.txt");
fastml-3.11/www/fastml/FastML_Wrapper.pl-586-
fastml-3.11/www/fastml/FastML_Wrapper.pl:587: system ("cp $VARS{tree_ancestor} $FORM{outDir}Tree_in_Ancestor_format.txt");
fastml-3.11/www/fastml/FastML_Wrapper.pl:588: system ("zip -r $FORM{outDir}$VARS{All_Outputs_Zip} Tree_in_Ancestor_format.txt; rm -f $FORM{outDir}Tree_in_Ancestor_format.txt");
fastml-3.11/www/fastml/FastML_Wrapper.pl-589-
##############################################
fastml-3.11/www/fastml/FastML_Wrapper.pl-681- chdir $VARS{send_email_dir};
fastml-3.11/www/fastml/FastML_Wrapper.pl:682: my $email_system_return = `$msg`;
fastml-3.11/www/fastml/FastML_Wrapper.pl-683- unless ($email_system_return =~ /successfully/) {
##############################################
fastml-3.11/www/fastml/FastML_Wrapper.pl-699- print "$RAxML_cmd\n";# <STDIN>;# DEBUG
fastml-3.11/www/fastml/FastML_Wrapper.pl:700: system($RAxML_cmd);
fastml-3.11/www/fastml/FastML_Wrapper.pl-701-
##############################################
fastml-3.11/www/fastml/FastML_Wrapper.pl-757- print "$fastml_comm\n";#<STDIN>;#DEBUG
fastml-3.11/www/fastml/FastML_Wrapper.pl:758: system ($fastml_comm);
fastml-3.11/www/fastml/FastML_Wrapper.pl-759-
##############################################
fastml-3.11/www/fastml/FastML_Wrapper.pl-794- print "$IndelReconstruction_cmd\n";# <STDIN>; #DEBUG
fastml-3.11/www/fastml/FastML_Wrapper.pl:795: system($IndelReconstruction_cmd);
fastml-3.11/www/fastml/FastML_Wrapper.pl-796- # CHECK FOR ERRORS
##############################################
fastml-3.11/www/fastml/FastML_Wrapper.pl-802- # Prepare JalView Outputs
fastml-3.11/www/fastml/FastML_Wrapper.pl:803:# system ("cp $FORM{outDir}/$VARS{tree_newick}.CODES $FORM{outDir}/$VARS{Tree_JalView}");
fastml-3.11/www/fastml/FastML_Wrapper.pl-804-# TreeCodesToNamesShort("$FORM{outDir}/$VARS{Tree_JalView}",$CodeToSeqName);
##############################################
fastml-3.11/www/fastml/FastML_Wrapper.pl-879- if ($ans ne "OK"){exit_on_error("sys_error","Make_JalView_AnnotGraph_JointProb($FORM{outDir}/$VARS{prob_joint},$FORM{outDir}/$VARS{JalViewJointAnnotationGraphFile},Joint log likelihood): FAILED: $ans");}
fastml-3.11/www/fastml/FastML_Wrapper.pl:880: #system ("cp $FORM{outDir}/$VARS{tree_newick} $FORM{outDir}/$VARS{Tree_JalView}");
fastml-3.11/www/fastml/FastML_Wrapper.pl-881- #FixTreeNamesForJalView("$FORM{outDir}/$VARS{Tree_JalView}");
##############################################
fastml-3.11/www/fastml/FastML_Wrapper.pl-1066- chdir $VARS{send_email_dir};
fastml-3.11/www/fastml/FastML_Wrapper.pl:1067: my $email_system_return = `$msg`;
fastml-3.11/www/fastml/FastML_Wrapper.pl-1068- unless ($email_system_return =~ /successfully/) {
##############################################
fastml-3.11/www/fastml/FastML_Wrapper.pl-1086- chdir $VARS{send_email_dir};
fastml-3.11/www/fastml/FastML_Wrapper.pl:1087: my $email_system_return = `$msg`;
fastml-3.11/www/fastml/FastML_Wrapper.pl-1088- print LOG "RESULT: $email_system_return\n";
##############################################
fastml-3.11/www/fastml/kMostProbSeq.pl-32-my $cmd="$K_MOST_PROB_SEQ -i $ProbMatrix -o $OutSeq -k $k";
fastml-3.11/www/fastml/kMostProbSeq.pl:33:system ($cmd);
fastml-3.11/www/fastml/kMostProbSeq.pl-34-
##############################################
fastml-3.11/www/fastml/IndelReconstruction_Wrapper.pl-157-
fastml-3.11/www/fastml/IndelReconstruction_Wrapper.pl:158:system ("cd $Indels_Reconstruction_results_Dir; $IndelCoder $IndelCoderParamFile");
fastml-3.11/www/fastml/IndelReconstruction_Wrapper.pl-159-
##############################################
fastml-3.11/www/fastml/IndelReconstruction_Wrapper.pl-176-close (INDEL_RECONSTRUCTION_PARAMS);
fastml-3.11/www/fastml/IndelReconstruction_Wrapper.pl:177:system ("cd $Indels_Reconstruction_results_Dir; $IndelReconstruction $IndelReconstructionParamFile");
fastml-3.11/www/fastml/IndelReconstruction_Wrapper.pl-178-my %MSA_Pos_Species_to_Indel=();
##############################################
fastml-3.11/www/fastml/BuildRaxMLTree.pl-28-#my $convert_cmd="readseq -a -f12 $CodedMSA > $CodedMSAPhylip";
fastml-3.11/www/fastml/BuildRaxMLTree.pl:29:#system ($convert_cmd);
fastml-3.11/www/fastml/BuildRaxMLTree.pl-30-# Run RaxML
##############################################
fastml-3.11/www/fastml/BuildRaxMLTree.pl-33-print "$RaxML_cmd\n";
fastml-3.11/www/fastml/BuildRaxMLTree.pl:34:system ($RaxML_cmd);
fastml-3.11/www/fastml/BuildRaxMLTree.pl-35-# Bring Back names to tree
##############################################
fastml-3.11/www/bioSequence_scripts_and_constants/GENERAL_CONSTANTS.pm-240- if ($email_attach ne '') {$mail.=" -a $email_attach";}
fastml-3.11/www/bioSequence_scripts_and_constants/GENERAL_CONSTANTS.pm:241: `$mail`;
fastml-3.11/www/bioSequence_scripts_and_constants/GENERAL_CONSTANTS.pm-242-}
##############################################
fastml-3.11/www/bioSequence_scripts_and_constants/GENERAL_CONSTANTS.pm-344- $mail = 'sh -c \' $mail 2>/dev/null\'';
fastml-3.11/www/bioSequence_scripts_and_constants/GENERAL_CONSTANTS.pm:345: `$mail`;
fastml-3.11/www/bioSequence_scripts_and_constants/GENERAL_CONSTANTS.pm-346-}
##############################################
fastml-3.11/debian/createmanpages-4-
fastml-3.11/debian/createmanpages:5:VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
fastml-3.11/debian/createmanpages-6-