dDocent run started Thu Oct 17 17:09:43 PDT 2019 

At this point, all configuration information has been entered and dDocent may take several hours to run.
It is recommended that you move this script to a background operation and disable terminal input and output.
All data and logfiles will still be recorded.
To do this:
Press control and Z simultaneously
Type 'bg' without the quotes and press enter
Type 'disown -h' again without the quotes and press enter

Now sit back, relax, and wait for your analysis to finish

Using FreeBayes to call SNPs

Using VCFtools to parse TotalRawSNPS.vcf for SNPs that are called in at least 90% of individuals
WARNING: RunAsUser for MSP ignored, check group ids (egid=20746, want=51)
can not chdir(/var/spool/clientmqueue/): Permission denied
Program mode requires special privileges, e.g., root or TrustedUser.