kma install issue

[Jessica Rowell]

I followed the exact installation instructions. I ran make inside ~/resfinder/cge/kma. Then I installed the resfinder database. Then I tried to index the database with KMA. I navigated to db_resfinder and ran python3 INSTALL.py. I got the message mentioned in the instructions that suggests that kma_index wasn’t found. I followed the instructions exactly.

Should I have run make install in addition to make for kma? One thing I can think of is that the place where I ran git clone https://[e-mail]/genomicepidemiology/resfinder.git` itself is not on my path. Does the resfinder directory itself need to be on my path?

Thank you for your help!

[Jessica Rowell]

I get the same message if I explicitly specify the PATH to kma_index (I see the executable there too), like this:

python3 INSTALL.py /home/jess/data/resfinder/cge/kma

[CGE Helpdesk]

Dear Jessica,

Thank you for the interests in our services and for your message.

There are different ways you can install and index the databases with kma. If you use python3 INSTALL.py without any path, two options should come up: 1. and 2. Then, if you choose 1., (just write 1 and and enter in the command line), the databases will be indexed with kma.

You can also specify the path as you suggest, however, the path should point to kma_index, meaning that in your case that would be python3 INSTALL.py /home/jess/data/resfinder/cge/kma/kma_index

I hope this answers your question, otherwise please do not hesitate to write us again.

Kind regards,

Malene, CGE Helpdesk

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[Safina A.R]

Im still getting errors on the test script even after running all the suggested commands. the error is :

======================================================================

ERROR: test_on_data_with_just_point_mut_using_kma (main.ResFinderRunTest)

Traceback (most recent call last):
File "tests/functional_tests.py", line 254, in test_on_data_with_just_point_mut_using_kma
check=True)
File "/home/sar/miniconda3/lib/python3.6/subprocess.py", line 438, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command 'python3 /home/sar/resfinder/run_resfinder.py -ifq data/test_isolate_05_1.fq data/test_isolate_05_2.fq -o running_test/test4 -s 'Escherichia coli' --min_cov 0.6 --threshold 0.8 --point --db_path_point /home/sar/resfinder/db_pointfinder --db_path_res /home/sar/resfinder/db_resfinder --kmaPath /home/sar/resfinder/cge/kma/kma' returned non-zero exit status 1.

---

Ran 4 tests in 2.657s

FAILED (errors=1)

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Can you please help

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I have ran it even mentioning path as well

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[Jane Lucas]

I am having similar issues. Jessica, were you able to figure this out? I am continually getting the error of kma_index command not found

[Hanjié Wu]

Hi, I ran make inside ~/resfinder/cge/kma and got the following error message:

cc -Wall -O3 -std=c99   -c -o align.o align.c

cc -Wall -O3 -std=c99   -c -o alnfrags.o alnfrags.c

In file included from alnfrags.h:24:0,

from alnfrags.c:23:

filebuff.h:21:18: fatal error: zlib.h: No such file or directory

compilation terminated.

<builtin>: recipe for target 'alnfrags.o' failed

make: *** [alnfrags.o] Error 1

please help, thanks

[CGE Helpdesk]

Dear Safina,

Thank you for the interests in our services.

It looks like 3/4 of the tests succeeds. In order to figure out why one of the tests fails, could you please run the command that fails (but make sure that the paths are the correct paths relative to the directory from where you run the tests).

Like this (you might need to change the paths in this example according to your own)

cd /path/to/resfinder

python3 run_resfinder.py -ifq tests/data/test_isolate_05_1.fq tests/data/test_isolate_05_2.fq -o running_test/test4 -s 'Escherichia coli' --min_cov 0.6 --threshold 0.8 --point --db_path_point db_pointfinder --db_path_res db_resfinder --kmaPath cge/kma/kma

The command is essentially the same as the one that fails in your case, but when it is run outside the functional_tests.py script, it will presumably give a more informative error message. If you receive an error message, could you please pass it, then we will take a look at it.

Kind regards

Malene, CGE Helpdesk

[CGE Helpdesk]

Dear Jane Lucas,

Thank you for the interest in our services.

When installing ResFinder and running the tests, the tests will only succeed if both Blastn and KMA is installed. Please make sure that both of these are installed according to the instructions in the README of ResFinder here: https://bitbucket.org/genomicepidemiology/resfinder/src/master/

If kma_index is not found, it sounds like KMA is not installed or the path to kma_index is wrong. Is it this message you get, when you try to install the databases: ?

KMA index program, kma_index, does not exist or is not executable
Please input path to executable kma_index program or choose one of the options below:
    1. Install KMA using make, index db, then remove KMA.
    2. Exit

If yes, then the easiest way to install the database is by pressing 1 and enter.

If this does not help, please do not hesitate to write again.

Kind regards

Malene, CGE helpdesk.

[CGE Helpdesk]

Dear Hanjié Wu,

Thank you for the interest in our services.

I have spoken to the developer of KMA, and it looks like zlib development files are missing. These can be installed with:

sudo apt-get install libz-dev

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

Kind regards,

Malene, CGE Helpdesk.

[Peter Cock]

If you are using conda with the bioconda channel, you can use conda install kma for this dependency (and conda install blast etc).