can not use pointfinder

[Former user]

hi, thank you for the development of this tool. when i use the db_resfinder ,it is successful. python3 /resfinder/resfinder.py -i /GenomewithID/Sa16952.seq -o /1111/Sa16952 -p /resfinder/db_resfinder -x

but i can not use the db_pointfinder My command was as follows: ython3 /resfinder/run_resfinder.py -i /GenomewithID/Sa16952.seq -o /1111/Sa16952.seq -s "Escherichia coli" --point

Error is as follows: Traceback (most recent call last): File "/resfinder/run_resfinder.py", line 16, in <module> from cge.out.util.generator import Generator File "/resfinder/cge/out/util/generator.py", line 3, in <module> from git import Repo ModuleNotFoundError: No module named 'git'

another way: python3 /resfinder/resfinder.py -i /GenomewithID/Sa16952.seq -o /1111/Sa16952.seq -p /resfinder/db_pointfinder -x

Error is as follows: Input Error: notes.txt not found! (/resfinder/db_pointfinder/notes.txt)

I don't think I'm using it right ,and i reinstalled the program it is still not working Thank you in advance!

[CGE Helpdesk]

Dear user,

Thank you for the interest in our services and sorry for the late response.

It sounds like you did not install the module git. It can be installed by using the command:

pip3 install git

Did you install the pointfinder database as well? This database is necessary for detecting point mutations. The pointfinder database can be installed from here: https://bitbucket.org/genomicepidemiology/pointfinder_db/src/master/

I hope this helps, otherwise please do not hesitate to write us again.

Kind regards

Malene, CGE helpdesk

[Jessica Rowell]

Hi,

I’m wondering what was the resolution to the db_pointfinder part of this issue? I’m having the same problem. I downloaded and kma-indexed db_pointfinder as instructed (and db_resfinder too). I look and the requested notes.txt file is indeed not there.

run_resfinder.py --version output is 4.1.11

I just downloaded and re-indexed both databases today.

‌

Update:

I was (accidentally) using the --acquired flag with run_resfinder.py and -s Klebsiella. This gave me the notes.txt not found error.

However, when I change it to --point I just get a different error: antibiotic_classes.txt not found.

Update2:

Ok I believe I have solved it. But I’ll leave this here because the series of errors I was getting is a little bit strange. The problem was I was using

-db_res home/ref/db_resfinder

instead of

--db_path_point /home/ref/db_pointfinder --db_path_res /home/ref/db_resfinder

Sorry for the trouble! I’ll leave it here in case others stumble on the same user error.