I tried to use the build-species module but it fails always with
"ERROR: At least, a complete reference genome is required to reorder contigs of draft genomes".
There are definitely complete reference genomes consisting of only one Contig available in the specified genomes folder. I tried to extract the file "num_of_contigs.txt" and it appears to have only one column containing the names of the fasta-files however there's no value for the number of contigs in this file. The second columns is missing completely, which is likely the reason why the program fails.
Command used to run the build-species module:
smeg build_species -g ../Lactobacillus_murinus/ -o Lactobacillus_murinus_SMEGdb -a
Installation was done via conda, running on a fresh install of Ubuntu 18.04.4.
I tried to use the build-species module but it fails always with "ERROR: At least, a complete reference genome is required to reorder contigs of draft genomes".
There are definitely complete reference genomes consisting of only one Contig available in the specified genomes folder. I tried to extract the file "num_of_contigs.txt" and it appears to have only one column containing the names of the fasta-files however there's no value for the number of contigs in this file. The second columns is missing completely, which is likely the reason why the program fails.
Command used to run the build-species module: smeg build_species -g ../Lactobacillus_murinus/ -o Lactobacillus_murinus_SMEGdb -a
Installation was done via conda, running on a fresh install of Ubuntu 18.04.4.