Question: Help to run Kaiju through command line interface
0
gravatar for dinakaran.svgev
5 weeks ago by
dinakaran.svgev0 wrote:

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.

sequencing next-gen kaiju • 124 views
ADD COMMENTlink modified 5 weeks ago by genomax87k • written 5 weeks ago by dinakaran.svgev0
1

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

ADD REPLYlink written 5 weeks ago by antonioggsousa860

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

ADD REPLYlink written 5 weeks ago by dinakaran.svgev0

Hi,

You can add comments rather than answers.

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

António

ADD REPLYlink written 5 weeks ago by antonioggsousa860

Thanks for your reply.

ADD REPLYlink written 5 weeks ago by dinakaran.svgev0

Hi, The output of that command line was killed

ADD REPLYlink written 5 weeks ago by dinakaran.svgev0

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

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by Sej Modha4.7k

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

ADD REPLYlink written 5 weeks ago by antonioggsousa860
1
gravatar for genomax
5 weeks ago by
genomax87k
United States
genomax87k wrote:

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.

ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by genomax87k
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