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chasewnelson / SNPGenie

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
GNU General Public License v3.0
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Empty output / wrong VCF file? #8

Closed WardDeb closed 6 years ago

WardDeb commented 6 years ago

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:

################################################################################
##                                                                            ##
##                             SNPGenie Initiated!                            ##
##                                                                            ##
################################################################################

  ###############################  LICENSE:  #################################
  ##            SNPGenie Copyright (C) 2015-18 Chase W. Nelson              ##
  ##            This program comes with ABSOLUTELY NO WARRANTY;             ##
  ##     This is free software, and you are welcome to redistribute it      ##
  ##               under certain conditions; see LICENSE.txt.               ##
  ############################################################################

You have not selected a MIN. MINOR ALLELE FREQ. All variants in the SNP report(s) will be included.

Reading in FASTA file... COMPLETED.

Indexing sequence... COMPLETED.

################################################################################
##                      SNPGenie completed successfully.                      ##
##             Please find results in the SNPGenie_Results folder.            ##
################################################################################

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

singing-scientist commented 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., #CHROMPOSID...). I have implemented a warning to alert the user when this is the case. Please let me know if you still encounter any problems when the header is included.

Best, Chase

WardDeb commented 6 years ago

Thanks @cwnelson88,

Rerunning with header seems to have fixed the problem. Output looks as expected now.

Thanks for the quick response!