error with metator host command

[meltzj]

Hi there,

I'm trying to use the metator host command after running metator.
metator host --network=/path/to/network.txt --binning=/path/to/binning.txt --mges=/path/to/list_of_mges.txt --contig-data=/path/to/final/contig_data_final.txt

where network.txt, binning.txt and contig_data_final.txt are the output files after running metator pipeline.

This is the following error I get:
INFO ::

Traceback (most recent call last):
File "/srv/scratch/z5116142/miniconda3/envs/metator_1/bin/metator", line 8, in
sys.exit(main())
File "/srv/scratch/z5116142/miniconda3/envs/metator_1/lib/python3.10/site-packages/metator/main.py", line 63, in main
command.execute()
File "/srv/scratch/z5116142/miniconda3/envs/metator_1/lib/python3.10/site-packages/metator/commands.py", line 1454, in execute
mth.host_detection(
File "/srv/scratch/z5116142/miniconda3/envs/metator_1/lib/python3.10/site-packages/metator/host.py", line 280, in host_detection
count = sub.getBinScore()
File "/srv/scratch/z5116142/miniconda3/envs/metator_1/lib/python3.10/site-packages/metator/host.py", line 132, in getBinScore
if score >= self.threshold:
TypeError: '>=' not supported between instances of 'float' and 'str'

Any suggestions?

[mmarbout]

Hi .
We do not often use the metator host command and rather use the whole pipeline metator mge to directly bin mge-contig and then assign their host(s). I have reproduced your error and will try to fix the problem in a next release of metator. For the moment, you can use the metator mge command that works without problems from my side.

Martial

[meltzj]

I've seen that you have now updated the host module in the latest update.
I've installed the updated version in conda but am now getting this error:

Traceback (most recent call last):
File "/srv/scratch/z5116142/miniconda3/envs/metator_1.3.10/bin/metator", line 11, in
sys.exit(main())
^^^^^^
File "/srv/scratch/z5116142/miniconda3/envs/metator_1.3.10/lib/python3.11/site-packages/metator/main.py", line 63, in main
command.execute()
File "/srv/scratch/z5116142/miniconda3/envs/metator_1.3.10/lib/python3.11/site-packages/metator/commands.py", line 1454, in execute
mth.host_detection(
^^^^^^^^^^^^^^^^^^
AttributeError: module 'metator.host' has no attribute 'host_detection'

[js2264]

Hi @meltzj,
We are currently implementing the host module so that it is is available from command line, but it still needs some work and is currently not functional. The module also requires the mge module to be fully functional, and we spotted other bugs there too. I can ping you when bugs are fixed. Sorry for the inconvenience.

[meltzj]

Hi there! Just checking in to see how you guys are going with this! Any updates?

[chenolaf]

I have the same trouble,Any updates?