Help to run Kaiju through command line interface

Question

[dinakaran.svgev]

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.

[antonioggsousa]

Hi,

Probably, it's due to limited RAM memory.

If you're running a linux distribution, can you try:

/usr/bin/time -v <your-kaiju-cmd-line-here>

Then, post the result here please.

António

[dinakaran.svgev]

/usr/bin/time -v kaiju -t nodes.dmp -f kaiju_db_nr_euk.fmi -i firstfile.fastq -j secondfile.fastq

[antonioggsousa]

Hi,

You can add comments rather than answers.

Ok, I see your command-line. What was the output of that command-line?

António

[dinakaran.svgev]

Thanks for your reply.

[dinakaran.svgev]

Hi, The output of that command line was killed

[Sej Modha]

Please use the ADD COMMENT box for discussion, the answer field is reserved for answers/solutions.

[antonioggsousa]

I think it shouldn't be killed because if you get an error it should print something like, even if gets killed:

Command exited with non-zero status 127
Command being timed: "lsn"
User time (seconds): 0.00
System time (seconds): 0.00
Percent of CPU this job got: ?%
Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.00
Average shared text size (kbytes): 0
Average unshared data size (kbytes): 0
Average stack size (kbytes): 0
Average total size (kbytes): 0
Maximum resident set size (kbytes): 1160
Average resident set size (kbytes): 0
Major (requiring I/O) page faults: 0
Minor (reclaiming a frame) page faults: 27
Voluntary context switches: 1
Involuntary context switches: 0
Swaps: 0
File system inputs: 0
File system outputs: 0
Socket messages sent: 0
Socket messages received: 0
Signals delivered: 0
Page size (bytes): 4096
Exit status: 127

Although, I'm not 100% sure. Anyway I believe that @genomax answer (below) answers your question.

António

Answer 1

[GenoMax]

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.