Good afternoon everybody.
I am new to next gen sequence analysis and also Linux. I am using abyss to assemble Illumina short read sequences. One problem i am facing that the output files of abyss assembly were present in the home directory but I want it to be present is a specific folder. Could anybody kindly help me pleas to resolve the issue.
First create your specific folder with mkdir "name_of_folder" an then redirect the output from abyss to the folder with > and the path of folder.
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This script will create specific directory for each kmer value:
#!/usr/bin/perl -w
use strict;
use warnings;
use Cwd;
my $usage = "usage: $0 ";
my $infile1 = shift or die "$usage\n";
my $infile2 = shift or die "$usage\n";
my $infile3 = shift or die "$usage\n";
my $infile4 = shift or die "$usage\n";
### create directories and run 'abyss_pe'
foreach my $hash_length qw(55 59 61 65 71 75 79 81 85 89 91) {
my $dirname = "$hash_length";
my $current_dir = getcwd;
mkdir($dirname) unless -d $dirname;
chdir($dirname);
system("ln -s ../$infile1 .") unless -e $infile1;
system("ln -s ../$infile2 .") unless -e $infile2;
system("ln -s ../$infile3 .") unless -e $infile3;
system("ln -s ../$infile4 .") unless -e $infile4;
#my $not_done=0;
#if (-s "./Sequences") {
#warn "'$dirname/Sequences' exists\n";
#} else {
# $not_done = 1;
# warn "'$dirname/Sequences'does not exist\n";
# }
# if (-s "./Roadmaps"){
#warn "'$dirname/Roadmaps' exists\n";
# } else {
# $not_done = 1;
# warn "'$dirname/Roadmaps'does not exist\n";
# }
# if (-s "./contigs.fa"){
# warn "'$dirname/contigs.fa' exists\n";
# $not_done = 0;
# } else {
#warn "'$dirname/contigs.fa'does not exist\n";
# }
# if ($not_done) {
# warn "'$dirname/Sequences' and/or '$dirname/Roadmaps' are absent\n";
my $cmd;
if ($infile1 =~ m/fastq|fasta|fa|txt|fq$/i && $infile2 =~ m/fastq|fasta|fa|txt|fq$/i ) {
# $cmd = '/path/to/abyss-pe . k=$hash_length n=10 in="$infile1 $infile2" name=abyss';
$cmd = 'source abyss_upTo95-1.3.3 ; abyss-pe k='$hash_length' n=10 np=8 name=Name_abyss-mpi_'$hash_length' mpirun=mpirun.lsf in='$infile1 $infile2 $infile3 $infile4'';
} else {
print"\n Please provide either fasta or fastq files\n";
}
my $bsub_cmd = 'bsub -a openmpi -R "rusage[mem=75000] span[ptile=8] " -n 8 '$cmd'';
#my $host_name = `hostname`;
#if ($host_name =~ m/jic54532/) {
warn "$bsub_cmd\n";
system($bsub_cmd);
#} else {
# warn "$cmd\n";
# system($cmd);
#}
# }
# else {
# warn "Skipping directory $dirname' because '$dirname/Roadmaps' and '$dirname/Sequences' exist\n";
# }
chdir($current_dir);
}
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