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carma3-SGE.pl
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#!/usr/bin/env perl
#
# Copyright (C) 2007 CeBiTec, Bielefeld University
# Written by Wolfgang Gerlach.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# version 2 as published by the Free Software Foundation.
#
# This file is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this file; see the file LICENSE. If not, write to
# the Free Software Foundation, Inc., 59 Temple Place - Suite 330,
# Boston, MA 02111-1307, USA.
#
use strict;
require Scheduler::DRMAA;
use FindBin;
use lib "$FindBin::Bin/lib/SplitFasta";
use lib "$FindBin::Bin/lib/Schedule";
use lib "$FindBin::Bin/lib";
use SplitFasta;
use FileUtils;
use File::Temp qw(tempfile tempdir);
use File::Glob ':glob';
use File::Copy;
use Getopt::Std;
use Cwd;
use File::Path;
1;
our($opt_p, $opt_P,$opt_M, $opt_h, $opt_c, $opt_l, $opt_m, $opt_x, $opt_n, $opt_d, $opt_a, $opt_e, $opt_I, $opt_C);
my $config_file = "carma.cfg";
my $prefix = "chunk_";
#defined by configuration file:
my $carma_binary;
#my $blastall_script;
#my $blastx_database;
#my $blastx_evalue;
#my $blastn_database;
#my $blastn_evalue;
my $cluster_tmp_dir;
my $maxNumberOfChunks;
my $message;
my $LD_LIBRARY_PATH;
my $clusteremail;
my $notificationemail;
############################
sub usage{
print STDERR <<USAGE;
Copyright (C) 2010 CeBiTec, Bielefeld University.
Written by Wolfgang Gerlach.
This software comes with ABSOLUTELY NO WARRANTY; This is free
software, and you are welcome to redistribute it under certain conditions.
Read the COPYRIGHT for details.
carma3-SGE.pl: taxonomic classification of short
environmental DNA fragments
Usage: carma3-SGE.pl <options> <fasta_input_file>
where: fasta_file contains metagenomic DNA-fragments
Options
-p <c> : project output directory (required)
-m : use Pfam HMM (for DNA)
-M : use Pfam HMM (for amino acids)
-x : use BLASTX
-P : use BLASTP
-c <n> : submit <n> jobs
-l <n> : at most <n> CPUs are used on the cluster
-d : delete intermediate results (e.g. BLAST result)
-a : configuration file
-C : pass to --config_overlay option (experimental)
-e <c> : email notification via UNIX "mail"
-h : show this help message
USAGE
}
sub DIE_handler {
my($signal) = @_;
my $mail_message = "CARMA3 pipeline failed";
if (defined $signal) {
$mail_message .= ": ".$signal;
}
mailme($mail_message);
}
$SIG{__DIE__} = 'DIE_handler';
sub mailme {
my ($mail_message) = @_;
if (defined $opt_e) {
my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst)=localtime(time);
my $timestamp = sprintf "%4d-%02d-%02d %02d:%02d:%02d", $year+1900,$mon+1,$mday,$hour,$min,$sec;
$mail_message = "[".$timestamp."] ".$mail_message;
my $mail_command = "echo \"Subject:CARMA3 job status notification\\n".$mail_message."\" \| mail ".$opt_e;
print STDERR "call: ".$mail_command."\n";
system( $mail_command );
}
}
my %config_file_hash;
sub readConfiguration {
my ($_config_file) = @_;
print $carma_binary."\n";
open(FILE,$_config_file) or die $!;
while (<FILE>) {
#print $_;
chomp($_);
if ($_ =~ /^#/) {
next;
}
if ($_ =~ /^\s*$/) {
next;
}
if (my ($key, $value) = $_ =~ /(\S+)\s*\=\s*(\S+)/) {
if (my ($inner_value) = $value =~ /^\"(\S*)\"$/ ) {
$value = $inner_value;
}
#print $key.": ".$value."\n";
$config_file_hash{$key} = $value;
} else {
die("Error parsing Configuration file: \"".$_."\"\n");
}
}
close (FILE);
# take values from configuration hash
$carma_binary = getConfigValue("carma_binary");
$clusteremail = getConfigValue("clusteremail");
#$blastall_script = getConfigValue("blastall_script");
#$blastx_database = getConfigValue("blast_nr_database");
#$blastn_database = getConfigValue("blast_nt_database");
#$blastx_evalue = getConfigValue("blastx_evalue");
#$blastn_evalue = getConfigValue("blastn_evalue");
$maxNumberOfChunks = getConfigValue("maxNumberOfChunks");
$message = getConfigValue("message");
$cluster_tmp_dir = getConfigValue("cluster_tmp_dir");
$LD_LIBRARY_PATH = getConfigValue("LD_LIBRARY_PATH");
}
sub getConfigValue() {
my ($key) = @_;
unless (defined $config_file_hash{$key}) {
die( "Error: Key \"".$key."\" not found in configuration file !\n");
}
return $config_file_hash{$key};
}
sub submit_SGE_jobs_meta{
my ($actual_command_line, $this_project_dir, $num_jobs, @l_options) = @_;
my $max_repeats = 5;
my $success_jobs = 0;
while ($success_jobs < $num_jobs && $max_repeats > 0) {
$success_jobs = submit_SGE_jobs($actual_command_line, $this_project_dir, $num_jobs, @l_options);
if ($success_jobs == $num_jobs) {
return 0;
}
print STDERR "Warning: Only $success_jobs of $num_jobs succeeded. Submit again... ($max_repeats)\n";
$max_repeats--;
sleep 10;
}
die ("Error: Cluster submission failed. Only $success_jobs of $num_jobs succeeded.\n");
return 1;
}
sub submit_SGE_jobs{
my ($actual_command_line, $this_project_dir, $num_jobs, %l_options) = @_;
my $stop_file = $this_project_dir."/../stop";
my $last_stop_test = time();
if (-e $stop_file) {
print STDERR "warning: stop file detected\n";
exit(0);
}
require Scheduler::DRMAA;
my @job_cmd_array;
my $template = "CARMA3_XXXXXX";
my ($fh, $script_file) = tempfile ($template, UNLINK => 1, DIR => $cluster_tmp_dir, SUFFIX => ".sh");
print STDERR "script_file: $script_file\n";
push(@job_cmd_array, $script_file );
open (MYFILE, '>'.$script_file) or die;
print MYFILE "#!/bin/bash\n";
print MYFILE "ulimit -c 0\n"; # to avoid huge dump cores
#print MYFILE "export LD_LIBRARY_PATH=".$LD_LIBRARY_PATH."\n";
print MYFILE $actual_command_line."\n";
close (MYFILE);
chmod(0775, $script_file);
# open file
#open (MYFILE, '<'.$script_file) or die;
#unlink $script_file;
sleep 10;
unless (-d $this_project_dir) {
print STDERR $message."project directory not found.\n";
exit(1);
}
#my $tmp_dir = FileUtils::get_tmp_dir_object($cluster_tmp_dir);
#my $errorfile = $this_project_dir."\$SGE\_TASK\_ID.stderr";
#delete old stderr-files:
my @old_stderr_files = glob $this_project_dir."*.stderr";
foreach my $file (@old_stderr_files) {
unlink $file or die "Could not unlink $file: $!";
}
my $scheduler = Scheduler::DRMAA->new(temp_dir => $this_project_dir, commandline => [@job_cmd_array]);
#my $native_options = "-cwd -l arch=sol-amd64,vf=20G";
my $native_options = "-cwd -l arch=sol-amd64";
while ( my ($key, $value) = each(%l_options)) {
$native_options.=",$key=$value";
}
unless (defined $opt_I) {
$native_options.=",idle=1";
}
if ( $clusteremail =~ /\@/ ) {
$native_options.=" -m a -M ".$clusteremail;
#$native_options.=" -m a -M wgerlach\@cebitec.uni-bielefeld.de";
}
if (defined $opt_l) { #max_running_tasks -- limit number of CPUs, not jobs
$native_options.=" -tc ".$opt_l;
}
#if ($LD_LIBRARY_PATH ne "") { #does not work!
# $native_options .= " -v LD_LIBRARY_PATH\=".$LD_LIBRARY_PATH;
#}
print STDERR "use native_options: $native_options\n";
$scheduler->set_native_option($native_options);
sleep 60; # 60 #work-around such that filesystem has time to sync..
my $jobids = $scheduler->submit2($num_jobs, 0);
my $arrayid = @$jobids[0];
($arrayid) = $arrayid =~ /^(\d+)\./;
print STDERR "Array job ID: ".$arrayid."\n";
print STDERR "Done.\nSubmitted $num_jobs jobs!\n";
system("echo $arrayid > ".$this_project_dir."/jobid.txt");
my @error_jobs=();
my $success_jobs = 0;
print STDERR "waiting and parsing results...\n";
$scheduler->iterate2(
sub {
my ($name) = @_;
$success_jobs++;
print STDERR "Job \"" . $name . "\" finished successfully. ";
if ($num_jobs != (@error_jobs+$success_jobs)) {
my $left = ($num_jobs-(@error_jobs+$success_jobs));
if ($left > 1) {
print STDERR "$left jobs are left.\n";
} else {
print STDERR "1 job is left.\n";
}
} else {
print STDERR "\n";
}
if (($last_stop_test + 600) >= time()) {
$last_stop_test = time();
if (-e $stop_file) {
print STDERR "warning: stop file detected\n";
exit(0);
}
}
},
sub {
my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst)=localtime(time);
printf STDERR "%4d-%02d-%02d %02d:%02d:%02d ", $year+1900,$mon+1,$mday,$hour,$min,$sec;
printf STDERR "Job $arrayid\.%s failed: %s\n",$_[0],$_[1];
push (@error_jobs, $_[0]);
if (($last_stop_test + 600) >= time()) {
$last_stop_test = time();
if (-e $stop_file) {
print STDERR "warning: stop file detected\n";
exit(0);
}
}
});
if (@error_jobs > 0) {
print STDERR "Sorry, list of jobs that failed: " . join(',', @error_jobs ) . "\n";
print STDERR "Command was: ".$actual_command_line."\n";
print STDERR $message."Cluster job crashed.\n";
#print STDERR "Simply rerun CARMA with same parameters, only jobs that failed will be resubmitted!\n";
#print STDERR "(Will not work if called via carma.pl using option \"-o\"!)\n";
#return 1;
} else {
print STDERR "All submitted jobs finished successfully!\n";
}
unlink $this_project_dir."/jobid.txt" or warn "Could not unlink ".$this_project_dir."/jobid.txt: $!";
unlink $script_file;
$scheduler->DESTROY();
# delete stdout-files, since they should be empty...
my @old_stdout_files = glob $this_project_dir."*.stdout";
foreach my $file (@old_stdout_files) {
unlink $file or die "Could not unlink $file: $!";
}
return $success_jobs;
}
sub makeDirectory{
my ($dir) = @_;
unless(-d $dir) {
print "create $dir\n";
mkdir $dir or die "Couldn't create dir: [$dir] ($!)";
}
}
sub getArrayMinPosition{
my ($array_ref) = @_;
my $size = @{$array_ref};
my $min_value=$$array_ref[0];
my $min_position=0;
for (my $i = 0; $i < $size; $i++) {
if ($$array_ref[$i] == 0) {
return $i;
}
if ($$array_ref[$i] < $min_value) {
$min_value = $$array_ref[$i];
$min_position=$i;
}
}
return $min_position;
}
sub mergeTaxFiles{
my ($output_dir, $result_file) = @_;
unless (-e $result_file) {
my $files_wildcard = "$output_dir/*.tax";
my @files = glob($files_wildcard);
unless (@files) {
print STDERR "ERROR: No (tax) result files found !??\n";
return 1;
}
unless (open(OUTPUT, ">".$result_file)) {
die $!;
}
foreach my $file (@files) {
#print $file."\n";
copy($file,\*OUTPUT);
}
close OUTPUT;
} else {
print STDERR "File \"$result_file\" already exists, skipping... \n";
}
return 0
}
sub combineTaxResultsByEvalue {
my $outputfile = shift(@_);
my @files = @_;
my @hashes;
my $superhash;
my $i=0;
# read files
foreach my $file (@files) {
print $file."\n";
unless (open(FILE, $file)) {
die $!;
}
while (<FILE>) {
#print $_;
chomp($_);
my ($desc, $prop, $goterms, $taxid, $tax_string, $evalue) = split(/\t/, $_);
my ($read_id) = $desc =~ /^(.*)\_-?\d\_-?\d$/;
unless ($read_id) {
$read_id = $desc;
}
#print $desc."\n";
$superhash->{$read_id} = 1;
if (defined $hashes[$i]->{$read_id}) {
die ( "already defined???\n");
}
$hashes[$i]->{$read_id} = [$desc, $prop, $goterms, $taxid, $tax_string, $evalue];
}
close(FILE);
$i++;
}
open(OUTFILE, ">".$outputfile) or die $!;
# iterate trough all reads
for my $key ( keys %$superhash ) {
#my $value = $superhash->{$key};
#print "$key => $value\n";
my $min_classi;
my $min_evalue=100000;
# my $count = 0;
foreach my $hash (@hashes) {
if (defined $hash->{$key}) {
#$count++;
#print $hash->{$key}[4]."\n";
if (($hash->{$key}[5] < $min_evalue) && ($hash->{$key}[5] > 0)) {
$min_evalue = $hash->{$key}[5];
$min_classi = $hash->{$key};
}
}
}
#print "max: $min_evalue\n";
if (defined $min_classi) {
print OUTFILE join("\t", @$min_classi)."\n";
}
#if ($count > 1) {
# print "c: $count\n";
# exit(0);
#}
}
close(OUTFILE);
}
sub combineTaxResults {
my $outputfile = shift(@_);
my @files = @_;
my @hashes;
my $superhash;
my $i=0;
open(OUTFILE, ">".$outputfile) or die $!;
# read files
foreach my $file (@files) {
print "read file: ".$file."\n";
unless (open(FILE, $file)) {
die $!;
}
while (<FILE>) {
#print $_;
chomp($_);
my ($desc, $prop, $goterms, $taxid, $tax_string, $evalue) = split(/\t/, $_);
my ($read_id) = $desc =~ /^(.*)\_-?\d\_-?\d$/;
unless ($read_id) {
$read_id = $desc;
}
#print $desc."\n";
unless (defined $superhash->{$read_id}) {
print OUTFILE $_."\n";
$superhash->{$read_id} = 1;
}
#if (defined $hashes[$i]->{$read_id}) {
# print STDERR "already defined???\n";
# abort();
#}
#$hashes[$i]->{$read_id} = [$desc, $prop, $goterms, $taxid, $tax_string, $evalue];
}
close(FILE);
$i++;
}
close(OUTFILE);
}
sub get_egt_by_family_hash {
my ($egt_result_file) = @_;
my $_egt_by_family_hash = {};
open(FILE, "<".$egt_result_file) or die $!;
my $pfam_family;
my $descr;
my $sequence ="";
while (<FILE>) {
#print $_;
chomp($_);
if ($_ =~ /^#/) {
next;
}
if ($_ =~ /^>/) {
($pfam_family) = $_ =~/^>(PF\d+\.\d+)\=\+\=/;
unless (defined $pfam_family) {
die("error parsing line:\n"."\"".$_."\"\n");
}
$descr = $_;
} else {
$sequence = $_;
push ( @{$_egt_by_family_hash->{$pfam_family}} , [$descr, $sequence]);
}
}
close (FILE);
return $_egt_by_family_hash;
}
sub collectEGTs() {
my ($_egt_result_file, $search_hmm_output_dir)= @_;
unless (-e $_egt_result_file) {
my $files_wildcard = "$search_hmm_output_dir/*.egt";
my @files = glob($files_wildcard);
unless (@files) {
print STDERR "ERROR: No EGT files found !??\n";
print STDERR $message."No homology could be detected.\n";
exit(0);
}
unless (open(OUTPUT, ">".$_egt_result_file)) {
die $!;
}
foreach my $file (@files) {
copy($file,\*OUTPUT);
}
close OUTPUT;
} else {
print STDERR "File \"$_egt_result_file\" already exists, skipping... \n";
}
my $egt_result_file_filesize = -s $_egt_result_file; //;;;
return $egt_result_file_filesize;
}
sub createNewEGTchunks {
my ($egt_by_family_hash, $classify_hmm_input_dir) = @_;
my $_realNumberOfEGTChunks;
my $numberOfFamilies = keys( %$egt_by_family_hash );
if ($numberOfFamilies < $maxNumberOfChunks) {
$_realNumberOfEGTChunks = $numberOfFamilies;
} else {
$_realNumberOfEGTChunks = $maxNumberOfChunks;
}
my $first_chunkfilename = $classify_hmm_input_dir.$prefix."1.egt";
if (-e $first_chunkfilename) {
print STDERR "EGT chunks already exist, skip creation...\n";
} else {
my @num_seq_per_file=();
my @egt_by_chunk=();
for (my $i=0; $i < $maxNumberOfChunks ;$i++) {
$num_seq_per_file[$i]=0;
}
foreach my $family (keys %{$egt_by_family_hash}){
my $array_ref = $egt_by_family_hash->{$family};
my $pos = getArrayMinPosition(\@num_seq_per_file);
my $num_egt_in_family = @{$array_ref};
$num_seq_per_file[$pos] += $num_egt_in_family;
push( @{$egt_by_chunk[$pos]}, @{$array_ref} );
}
for (my $i=0; $i < $_realNumberOfEGTChunks ;$i++) {
my $chunkfilename = $classify_hmm_input_dir.$prefix.($i+1).".egt";
#print "chunkfilename: $chunkfilename\n";
my $CHUNK_FILE;
open $CHUNK_FILE, ">>".$chunkfilename or die $!;
foreach my $tupel (@{$egt_by_chunk[$i]} ) {
my ($descr, $seq) = @{$tupel};
print $CHUNK_FILE $descr."\n";
print $CHUNK_FILE $seq."\n";
}
close($CHUNK_FILE);
}
}
return $_realNumberOfEGTChunks;
}
sub all_files_exist{
my ($path, $prefix, $suffix, $number) = @_;
my $all_exist = 1;
for (my $i = 1; $i <= $number; $i++) {
unless (-e $path.$prefix.$i.$suffix) {
$all_exist = 0;
last;
}
}
return $all_exist;
}
######################################################################################################################################
# START
require Scheduler::DRMAA;
# example:
#./carma3-SGE.pl -p /vol/cluster-data/wgerlach/test/ /vol/metagenomics/metagenomes/25genomes/metasim/25metagenome_454sim_default_formatted.fna
##################
# Get options
##################
getopts('p:PMc:l:hmxda:e:IC:');
####################
# check parameters
####################
unless(@ARGV==1){
usage;
print STDERR "FASTA input file is missing.\n";
exit 1;
}
unless(defined($opt_p)){
usage;
print STDERR "Argument \"-p\" is missing.\n";
exit 1;
}
my $project_dir = $opt_p;
my $first_char = substr($project_dir,0,1);
if ($first_char ne "/") {
print STDERR "error: please provide absolut path for project directory\n";
exit(1);
}
my $fasta_file=$ARGV[0];
unless(-e $fasta_file) {
print STDERR "ERROR: Could not read file \"$fasta_file\"!\n";
exit 1;
}
unless(defined($opt_m) || defined($opt_x) || defined($opt_n) || defined($opt_P)|| defined($opt_M)){
usage;
print STDERR "ERROR: give at leat one of the options -m, -x, -M or -P\n";
exit 1;
}
if ( (defined($opt_x) || defined($opt_m)) && defined($opt_P)) {
print STDERR "ERROR: combination of -P with others not supported\n";
exit 1;
}
if ( (defined($opt_x) || defined($opt_m)) && defined($opt_M)) {
print STDERR "ERROR: combination of -M with others not supported\n";
exit 1;
}
unless (-d $project_dir) {
die("Directory $project_dir not found.\n");
}
if (defined $opt_a) {
if (-e $opt_a) {
$config_file = $opt_a;
}
}
my $config_overlay_arg="";
if (defined $opt_C) {
$config_overlay_arg = " --config_overlay ".$opt_C." ";
}
################################
# config file
#make absolue path name:
unless (substr($config_file, 0, 1) eq "/") {
#my $thisdir = `pwd`;
my $thisdir = &Cwd::cwd();
$config_file = $thisdir."/". $config_file;
}
unless (-e $config_file) {
die("Configuration file \"$config_file\" not found..\n".
"Better provide full path to config file.\n")
}
readConfiguration($config_file);
if (defined $opt_c) {
$maxNumberOfChunks = $opt_c;
}
################################
# create project sub-directories:
my $last_char = substr($project_dir,-1,1);
if ($last_char ne "/") {
$project_dir .= "/";
}
my $search_input_dir = $project_dir."search_input/";
my $search_hmm_output_dir = $project_dir."search_hmm_output/";
my $search_blastx_output_dir = $project_dir."search_blastx_output/";
my $search_blastn_output_dir = $project_dir."search_blastn_output/";
my $search_blastp_output_dir = $project_dir."search_blastp_output/";
my $classify_hmm_input_dir = $project_dir."classify_hmm_input/";
my $classify_blastx_input_dir = $search_blastx_output_dir;
my $classify_blastn_input_dir = $search_blastn_output_dir;
my $classify_blastp_input_dir = $search_blastp_output_dir;
my $classify_hmm_output_dir = $project_dir."classify_hmm_output/";
my $classify_blastx_output_dir = $project_dir."classify_blastx_output/";
my $classify_blastn_output_dir = $project_dir."classify_blastn_output/";
my $classify_blastp_output_dir = $project_dir."classify_blastp_output/";
unless(-d $search_input_dir) {
mkdir $search_input_dir or die "Couldn't create dir: [$search_input_dir] ($!)";
}
if ((defined $opt_m) || (defined $opt_M)) {
makeDirectory($search_hmm_output_dir);
makeDirectory($classify_hmm_input_dir);
makeDirectory($classify_hmm_output_dir);
}
if (defined $opt_x) {
makeDirectory($search_blastx_output_dir);
makeDirectory($classify_blastx_output_dir);
}
if (defined $opt_P) {
makeDirectory($search_blastp_output_dir);
makeDirectory($classify_blastp_output_dir);
}
if (defined $opt_n) {
makeDirectory($search_blastn_output_dir);
makeDirectory($classify_blastn_output_dir);
}
################################
#read fasta-file, distribute sequences into chunks:
my $realNumberOfFASTAChunks = SplitFasta::splitFasta($maxNumberOfChunks, $fasta_file, $search_input_dir, $prefix);
if ($realNumberOfFASTAChunks == -1) {
print STDERR $message."No FASTA-sequence found!\n";
die;
}
################################
#submit search jobs:
if (defined $opt_x) {
# ---------------------------------------------------------------------------------------------------------------
# search-blastx:
my $all_exist = all_files_exist($search_blastx_output_dir, $prefix, ".blastx", $realNumberOfFASTAChunks);
if ($all_exist == 1) {
print STDERR "BLASTX results already there...\n";
} else {
print STDERR "Submit jobs for BLASTX search...\n";
my $blastx_search_command = $carma_binary.
$config_overlay_arg.
" --error ".$search_blastx_output_dir.$prefix."\$SGE_TASK_ID.stderr".
" --config ".$config_file.
" --local --delay \$SGE_TASK_ID".
" --blast --type n --database p --input ".$search_input_dir.$prefix."\$SGE_TASK_ID.fas".
" --output ".$search_blastx_output_dir.$prefix."\$SGE_TASK_ID.blastx";
print STDERR "blastx_search_command: $blastx_search_command\n";
my $ret = submit_SGE_jobs_meta($blastx_search_command, $search_blastx_output_dir, $realNumberOfFASTAChunks);
if ($ret == 1) {
print STDERR "Since blastx crashed, I delete all results...\n";
my $rm_command = "rm ".$search_blastx_output_dir.$prefix."\*\.blastx";
system($rm_command);
die;
}
}
# ---------------------------------------------------------------------------------------------------------------
# classify-blastx (blastx):
my $all_exist = all_files_exist($classify_blastx_output_dir, $prefix, ".tax", $realNumberOfFASTAChunks);
if ($all_exist == 1) {
print STDERR "blastx tax results already there...\n";
} else {
my $blastx_classify_command = $carma_binary.
$config_overlay_arg.
" --error ".$classify_blastx_output_dir.$prefix."\$SGE_TASK_ID.stderr".
" --local --delay \$SGE_TASK_ID".
" --config ".$config_file.
" --classify-blast --type n --database p --input ".$classify_blastx_input_dir.$prefix."\$SGE_TASK_ID.blastx".
" --blast-egts ".$classify_blastx_output_dir.$prefix."\$SGE_TASK_ID.blastxegt".
" --output ".$classify_blastx_output_dir.$prefix."\$SGE_TASK_ID.tax";
print STDERR "blastx_classify_command: $blastx_classify_command\n";
my $ret = submit_SGE_jobs_meta($blastx_classify_command, $classify_blastx_output_dir,$realNumberOfFASTAChunks, 'vf' => '20G');
if ($ret == 1) {
die;
}
}
}
if (defined $opt_P) {
# ---------------------------------------------------------------------------------------------------------------
# search-blastp:
my $all_exist = all_files_exist($search_blastp_output_dir, $prefix, ".blastp.gz", $realNumberOfFASTAChunks);
if ($all_exist == 1) {
print STDERR "BLASTP results already there...\n";
} else {
print STDERR "Submit jobs for BLASTP search...\n";
my $blastp_search_command = $carma_binary.
$config_overlay_arg.
" --error ".$search_blastp_output_dir.$prefix."\$SGE_TASK_ID.stderr".
" --config ".$config_file.
" --local --delay \$SGE_TASK_ID".
" --blast --type p --database p --input ".$search_input_dir.$prefix."\$SGE_TASK_ID.fas".
" --gzip".
" --output ".$search_blastp_output_dir.$prefix."\$SGE_TASK_ID.blastp.gz";
print STDERR "blastp_search_command: $blastp_search_command\n";
my $ret = submit_SGE_jobs_meta($blastp_search_command, $search_blastp_output_dir, $realNumberOfFASTAChunks);
if ($ret == 1) {
print STDERR "Since blastp crashed, I delete all results...\n";
my $rm_command = "rm ".$search_blastp_output_dir.$prefix."\*\.blastp";
system($rm_command);
die;