dDocent version 2.7.8 started Tue Dec 3 11:41:16 PST 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

Trimming reads and simultaneously assembling reference sequences

dDocent assembled 95067 sequences (after cutoffs) into 25196 contigs

Using BWA to map reads

Creating alignment intervals

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.