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elizabethmcd / metabolisHMM

Tool for constructing phylogenies and summarizing metabolic characteristics based on curated and custom profile HMMs
GNU General Public License v3.0
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Hmmsearch crashes at search-custom-markers #53

Closed nikobiota closed 3 years ago

nikobiota commented 3 years ago

Hi there,

Thanks for the tool! I installed it via conda and am trying to run a custom marker search with the code search-custom-markers --input genomes/ --output output_t6ss/ --markers_dir profiles/ --markers_list t6ss --metadata metadata.csv --summary sum.csv --heatmap heat.pdf --kofam ON --ko_list ko_list which results in the error below after the genome conversion. Any suggestion as how to fix would be appreciated!

metabolisHMM v2.21 Reformatting fasta files... Running HMM searches using custom marker set... Traceback (most recent call last): File "/home/niko/miniconda2/envs/metabolishmm/bin/search-custom-markers", line 4, in import('pkg_resources').run_script('metabolisHMM==2.22', 'search-custom-markers') File "/home/niko/miniconda2/envs/metabolishmm/lib/python3.9/site-packages/pkg_resources/init.py", line 665, in run_script self.require(requires)[0].run_script(script_name, ns) File "/home/niko/miniconda2/envs/metabolishmm/lib/python3.9/site-packages/pkg_resources/init.py", line 1463, in run_script exec(code, namespace, namespace) File "/home/niko/miniconda2/envs/metabolishmm/lib/python3.9/site-packages/metabolisHMM-2.22-py3.9.egg/EGG-INFO/scripts/search-custom-markers", line 188, in cmd = ["hmmsearch","-T"+tc,"--tblout="+outname,infile,genome] TypeError: can only concatenate str (not "NoneType") to str

elizabethmcd commented 3 years ago

Just to double check - did you download the HMM profiles from the KofamKoala distribution, including the ko_list file? The threshold cutoff score should be coming from the ko_list file since the HMMs within the KofamKoala distribution don't have the TC written in the HMM file itself. Otherwise it might be an issue with how this program runs the hmmsearch command, so I will double check on that end as well.

elizabethmcd commented 3 years ago

I just tested this version with a set of HMMs from the KofamKoala distribution, and it passes the hmmsearch step and runs to completion. It might be that whatever is in your t6ss list isn't in the profiles folder that came with the KofamKOALA distribution, and therefore doesn't have a TC score in the ko_list file. Try checking this or how you have your t6ss file formatted. It should look like for example:

K00022.hmm
K00232.hmm
K00249.hmm
K00255.hmm
K00632.hmm

Where .hmm is included for every KO file in the list.

nikobiota commented 3 years ago

Thanks a lot for the rapid reply, much appreciated! Reading your reply made me immediately feel dumb, cause indeed the .hmm was not included in my marker list :D Now it runs without any issues, so thanks again for helping me!