kma ended abruptly saying killed: 9.

[Former user]

I am trying to run thw following command:

kma -ipe R1.fastq.gz R2.fastq.gz -t_db /ncbi_nt -o out_kma/

But it ended abruptly with the following error:

Reading inputfile: R1.fastq.gz R2.fastq.gz

Phred scale: 33

Running KMA.

Killed: 9

[ptlcc]

It is the system that kills the process, probably because it uses too much memory.

Adding the “-mem_mode“ option will decrease the memory consumption significantly.

Best,
Philip

[vasudha jain]

still giving the same error.

[vasudha jain]

is there any other way to decrease the memory consumption?

[ptlcc]

That depends on how the database was indexed. It seems like it does not get to load the database, the *.comp.b file will be loaded into memory at startup.

Best,
Philip

[vasudha jain]

is there any --verbose option to check if this step is happening?

or are the details given in log file? if yes, how can I mention the path to save the log file at a particular directory?

‌

[ptlcc]

It will report it to stderr with something like:

# Total time used for DB loading: 0.01 s.

Best,
Philip

[vasudha jain]

there’s no log file being generated.

only four files are formed: out.aln, out.frag.gz, ouot.fsa, out.res.

and all of them are empty.

giving the erroe: killed 9

[vasudha jain]

I made a few changes to my command:

kma -t 8 -ipe Sample_R1.fastq.gz Sample_R2.fastq.gz -o path/to/output -t_db /ncbi_nt/ncbi_nt -verbose -mem_mode -and -apm f 

[ptlcc]

It is reported to stderr, i.e. the screen unless redirected.
How big is the database files, and how much memory do you have available.

Best,
Philip