kma issue

[xichuan Zhai]

Hi everyone,

I am a new user, and not sure how to “index your database using the kma_index file” before running Resfinder. I ran the following:

python3 run_resfinder.py -ifq tests/data/test_isolate_01_* -o outdir -s "Escherichia coli" -k kma/kma -l 0.6 -t 0.8 -acq -c

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and got:

Error: KMA did not run as expected.
KMA finished with the following response:

Segmentation fault (core dumped)

Best,

Xichuan

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[CGE Helpdesk]

Dear Xichuan,

Thank you for the interest in our services.

When you have downloaded the databases, you should index both the resfinder database and the pointfinder database as described in the readme section “Indexing databases with kma”.

It can be done by entering your local database repository and then use the INSTALL.py script like so:

# Go to the database directory
cd path/to/db_resfinder
python3 INSTALL.py

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I hope this solves your problem, otherwise please do not hesitate to write us again.

Kind regards,

Malene, CGE Helpdesk

[xichuan Zhai]

Thanks