dDocent run started Tue Nov 26 04:33:20 PST 2019 The configuration file config_cragig.txt does not exist. dDocent run started Tue Nov 26 04:36:34 PST 2019 The configuration file config_cragig.txt does not exist. dDocent run started Tue Nov 26 04:38:06 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 mawk: cannot open uniq.fq1 (No such file or directory) dDocent assembled 95067 sequences (after cutoffs) into 0 contigs Using BWA to map reads Creating alignment intervals mawk: cannot open reference.fasta.fai (No such file or directory) Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. Error: The genome file genome.file has no valid entries. Exiting. ***** ***** ERROR: Requested column 4, but database file - only has fields 1 - 0. 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.