dDocent run started Wed Oct 9 12:32:37 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
ls: cannot access *-RG.bam: No such file or directory
[E::hts_open_format] Failed to open file cat-RRG.bam
samtools index: failed to open "cat-RRG.bam": No such file or directory
Error: Unable to open file cat-RRG.bam. Exiting.
head: cannot open ‘reference.fasta’ for reading: No such file or directory
grep: reference.fasta: No such file or directory
mawk: cannot open cov.stats (No such file or directory)
mawk: cannot open cov.stats (No such file or directory)
mawk: cannot open cov.stats (No such file or directory)

Using FreeBayes to call SNPs
ls: cannot access mapped.*.bed: No such file or directory
rm: cannot remove ‘mapped.*.bed’: No such file or directory
could not open "raw.*.vcf" exiting
mv: cannot stat ‘raw.*.vcf’: No such file or directory

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.