Hi all, I am a post-doctoral fellow from India. When I am running kaiju through command line interface, the process gets killed at the Running kaiju step. Until this step, everything is alright. I am not getting output exactly at this step and the process gets killed at this step. Why is this happening? Is this because of less RAM capacity? We are using a system with 4GB RAM processor and 1TB hard disk storage. Kindly reply. Please somebody help.
1 answer
As noted in this kaiju GitHub link running kaiju against nr-euk database needs 117G of RAM.
We are using a system with 4GB RAM processor and 1TB hard disk storage
You don't have enough resources to run kaiju on this machine. That is the reason your job likely gets killed.
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Hi,
Probably, it's due to limited RAM memory.
If you're running a linux distribution, can you try:
Then, post the result here please.
António
/usr/bin/time -v kaiju -t nodes.dmp -f kaiju_db_nr_euk.fmi -i firstfile.fastq -j secondfile.fastq
Hi,
You can add comments rather than answers.
Ok, I see your command-line. What was the output of that command-line?
António
Thanks for your reply.
Hi, The output of that command line was killed
Please use the
ADD COMMENTbox for discussion, the answer field is reserved for answers/solutions.I think it shouldn't be killed because if you get an error it should print something like, even if gets killed:
Although, I'm not 100% sure. Anyway I believe that @genomax answer (below) answers your question.
António