Hello,
I am trying to run velvetoptimiser using the perl system command my script is like this:
my @velvetcmd;
my $velvetpath="/opt/software/velvet/1.2.10/contrib/VelvetOptimiser-2.2.4/VelvetOptimiser.pl";
push @velvetcmd,$velvetpath;
my $velvetarg=" -v -s 27 -e 31 -f '-fastq -shortPaired $reportdir/velvet/$nameseq.shuffled.fastq.gz' -p $velvetdir/$nameseq\_assembly";
push @velvetcmd,$velvetarg;
my $velvetcmdstr= join (" ",@velvetcmd);
system ('perl',$velvetpath,$velvetcmdstr) or die ;
I have the error message from :
You must supply the velveth parameter line in quotes. eg -f '-short .....'
Usage: /opt/software/velvet/1.2.10/contrib/VelvetOptimiser-2.2.4/VelvetOptimiser.pl [options] -f 'velveth input line'
Thanks for helping
b
I am trying to run velvetoptimiser using the perl system command my script is like this:
my @velvetcmd;
my $velvetpath="/opt/software/velvet/1.2.10/contrib/VelvetOptimiser-2.2.4/VelvetOptimiser.pl";
push @velvetcmd,$velvetpath;
my $velvetarg=" -v -s 27 -e 31 -f '-fastq -shortPaired $reportdir/velvet/$nameseq.shuffled.fastq.gz' -p $velvetdir/$nameseq\_assembly";
push @velvetcmd,$velvetarg;
my $velvetcmdstr= join (" ",@velvetcmd);
system ('perl',$velvetpath,$velvetcmdstr) or die ;
I have the error message from :
You must supply the velveth parameter line in quotes. eg -f '-short .....'
Usage: /opt/software/velvet/1.2.10/contrib/VelvetOptimiser-2.2.4/VelvetOptimiser.pl [options] -f 'velveth input line'
Thanks for helping
b
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