I created GVL climb server from the Cardiff cloud system with Nullarbor pipeline already configured, however, When I executed nullarbor pipeline on more than 200 isolates whole genomes fastq files and notice two errors.
First, snippy tool in the pipeline did not detect any SNPs in any of the isolates. I tried using three different reference genomes(FM211187, ATCC_700669, tigre4) but the ouput was the same, no SNP was detected by snippy in the nullarboe pipeline. I upgraded brew and updated all the nullabor tools in the pipeline but could not get any SNPs
Secondly, tbl2san error below is the error Could not run command: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y ‘Annotated using prokka 1.12 from https://github.com/tseemann/prokka’ -Z ERR1065578/prokka/ERR1065578.err -i ERR1065578/prokka/ERR1065578.fsa
I tried the solution suggested in the community issues by still getting the same error
Please any help to will be very much welcome