cat slurm-1388268.out dDocent 2.7.6 Contact…


cat slurm-1388268.out
dDocent 2.7.6

Contact jpuritz@uri.edu with any problems

Checking for required software

All required software is installed!

dDocent run started Thu Oct 10 14:41:43 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

Trimming reads and simultaneously assembling reference sequences
mawk: cannot open uniq.fq1 (No such file or directory)

dDocent assembled 69805 sequences (after cutoffs) into 0 contigs

Using BWA to map reads

Creating alignment intervals

***** 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
0% 0:0=0s
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.