Not an issue - Valuable usage tips

[Tarasovk49]

1. Every tool mentioned is pretty easy installed with conda except for the tool MetaGeneMark.
2. When installing MetaGeneMark you'll face a lot of dependency conflicts if using conda as well as errors I was not able to solve during installation from source. Solution for me was to use the prebuilt code I found here: https://github.com/aghozlane/spasm/tree/master/MetaGeneMark/mgm
3. If your contigs were assembled not with MEGAHIT they most likely won't have fasta headers of such form:
   >k79_0 flag=1 multi=15.0412 len=1221
   and you will get a crash when the tool starts fetching k-mer sizes from fasta headers.
   Mine were assembled using Spades with k-mer sizes -k 21,33,55,77,99,127 so I just used the longest k-mer value for each contig - that is 127 nucleotides. The code you need to fix located here: condiga/lib/python3.12/site-packages/condiga_utils/contig_utils.py
   I just commented original line and added constant value of k-mer value:

k_val = 127
#k_val = int(re.search(r"%s(.*)%s" % (start_n, end_n), record_id).group(1))