Closed WardDeb closed 6 years ago
Thanks very much for using SNPGenie, @WardDeb !
It appears to be failing because there is no HEADER in the VCF file (i.e., #CHROM
Best, Chase
Thanks @cwnelson88,
Rerunning with header seems to have fixed the problem. Output looks as expected now.
Thanks for the quick response!
Hi,
I'm trying to run SNPgenie on a couple of sequences that I've mapped from different samples. I've called the SNPs using freebayes, and produced the GTF file using prodigal. I needed to tinker a little bit with the files, but I think at this point they should be ok to use. However when I run SNPgenie with following command:
snpgenie.pl --vcfformat=4 --snpreport=vcffile.vcf --fastafile=fastafile.fna --gtffile=gtffile.gtf
The Program runs, and I get immediattely following output:
However when I look into the results output, all the files are empty.. I'm a bit puzzled at what could be causing this, and I think the VCF file could be the problem? I've inserted the files in here for troubleshooting.
Thanks in advance!
Warddeb