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vrmarcelino / CCMetagen

Microbiome classification pipeline
GNU General Public License v3.0
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Run out of memory #19

Closed SethCommichaux closed 3 years ago

SethCommichaux commented 4 years ago

I'm trying to run CCMetagen (with option 2 database -- nt without environmental seqs) on a metagenomic fastq file that is 24GB. It runs out of memory during the kma stage even though I'm using 250 GB of RAM. I'm using the command recommended on this github "kma -i $SAMPLE -o sample_out_kma -t_db $db -t $th -1t1 -mem_mode -and". Do you have recommendations for reducing memory usage?

vrmarcelino commented 4 years ago

Hi!

I've asked for Philip's advice on this issue and he suggested trying with the flag "-status" and reducing the number of threads to one ("-t 1"). The "-status" flag makes kma use fork rather than threads when possible, which will cause a "hard" freeing of memory that might do the trick.

On a note - it is quite unsual for it to require this much memory. Are you working with Illumina or long-read data?

vrmarcelino commented 3 years ago

Closing due to inactivity, please re-open if the issue persist.