Problem
knot -r input_raw.fasta -c canu.contigs.fasta -g canu.contigs.gfa -o ./knot
snakemake ./knot_AAG.csv --configfile /Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/knot/config.yaml --config contigs=RT001_canu.contigs.fasta out_prefix=./knot contigs_graph=RT001_canu.contigs.gfa read_type=pb min_contig_length=100000 search_mode=base package_path=/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/knot/ raw_reads=rt001_pb_raw.fasta --snakefile /Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/knot/main.rules
Wildcard constraints in inputs are ignored.
Building DAG of jobs...
MissingInputException in line 15 of /Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/knot/AAG.rules:
Missing input files for rule filter_contigs:
knot_knot/contigs.fasta