Error: KMA did not run as expected

[Anto]

Hi Phillip,

I posted the below on the ResFinder page but since the issue is related to running KMA, I thought I’ll post it here too.

KMA seems to be running into a core-dumping issue when I’m trying to analyze my metagenomic paired-end reads (total=65 Mio reads) on ResFinder. 

I have already rerun ‘python3 INSTALL.py’ from inside db_resfinder and I did see filenames with suffix ‘.length.b’ being created there. Below is the command-line I used:

python3 /home/tools/resfinder/run_resfinder.py -o resfinder_output_reads -s “Other” -l 0.8 -t 0.9 --acquired -ifq ReadA_1.fastq ReadA_2.fastq -k /home/tools/resfinder/kma/kma

Below is the error message I got and under “KMA finished with the following response”, I found only a couple of blank lines. A core dumping file starting with 'core.XXXX” was found inside the main working directory after this error message was displayed.

“Error: KMA did not run as expected.

KMA finished with the following response:”

I tried to run the above on my computational cluster node with --mem=100G --cpus-per-task=12. Resfinder works fine for me though when running in BLAST mode with a metagenomic assembly fasta file as the input. Any help here would be appreciated.

In case you’re wondering how I installed KMA at the time of setting up of ResFinder, below is the recipe that I followed (as per your earlier suggestions):

git clone https://[e-mail]/genomicepidemiology/kma.git

cd kma

git checkout develop

make

# Added the kma PATH to my .bash_profile and sourced

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[ptlcc]

Hi Anto

This might be because you are using kma from the develop branch, it was only meant to debug and solve that issue.
The kma in the main branch should be working.

Best,
Philip

[Anto]

Thank you for your prompt response Phillip- much appreciated! I’m a bit confused now. The reason I went for the develop branch is cos' I couldn’t get the main branch version to work on my system but now I’m not sure how I can make ResFinder to run kma from the main branch?

[ptlcc]

Hi Anto

I updated the main branch with the patches so you can run that one too.
When you clone the repository it will be on the main branch, elsewhere you can go there with:

git checkout master
git pull

To go to master and pull all updates from bitbucket. Then it is just compiling as before (i.e. make and add to path).

Best,
Philip

[Anto]

Hi Phillip,

I now got what you meant and have setup a new kma installation from the main branch. I’m just waiting for cluster resources to become available at my end to test it out. I’ll post here my results and will close this ticket as soon as I see that the problem is fixed. Thank you so much for your amazing and super-prompt support!

[Anto]

This is now fixed. Many thanks Phillip!