Entering edit mode
5.6 years ago
bioinformatics98
•
0
Hi,
I keep getting this issue in seqmule:
ERROR: Failed to find vcf-stats.
Please use 'cd /home/CLSTR/user/software/seqmule/bin/secondary/../..' and then './Build installexes'
Progams in your PATH are NOT used by SeqMule.
at /home/CLSTR/user/software/seqmule/bin/secondary/stats line 1261.
----------ERROR----------
[ => SeqMule Execution Status: step 29 FAILED at Fri Feb 7 22:28:54 CST 2020, Extract variants in custom regions]
ERROR: command failed
/home/CLSTR/user/software/seqmule/bin/secondary/../../bin/secondary/worker /home/CLSTR/user/data/sample/seqmule.02092020.57459.logs 29 "/home/CLSTR/user/software/seqmule/bin/secondary/../../bin/seqmule stats -tmpdir /tmp -capture /home/CLSTR/user2/softwares/seqmule/database/hg19/hg19_Exon_V4.bed -vcf Sample_result/Sample_bwamem.merge.realn.recal.0_gatk_hc.vcf -p Sample_result/Sample_bwamem.merge.realn.recal.0_gatk_hc"
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
After fixing the problem, please execute 'cd /home/CLSTR/user/data/sample’ and 'seqmule run Sample.script' to resume analysis.
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
*This is what the code in seqmule around line 1261 looks like (line 1261 is in bold):*
sub getExe
{
for my $exename(@_)
{
if ($loc{$exename})
{
return $loc{$exename};
} else
{
**if(my $exepath=&SeqMule::Utils::search($install_dir,$exename))**
{
$loc{$exename}=$exepath;
return $exepath;
}
}
}
die "ERROR: Failed to find @_\n";
Please help me understand what this error means and how I can resolve it. Thank you!