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broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool
GNU General Public License v2.0
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Memory problem #167

Open Wanjie-Feng opened 5 months ago

Wanjie-Feng commented 5 months ago

I now have a genome, the size is 1G, my server memory is only 500G, any suggestions ? here are my commands

java -Xmx500G -jar ./pilon/pilon-1.24.jar \
    --genome polish_3_version.fa \
    --bam sorted.markdup.q10.bam \
    --output refined \
    --outdir ./polish2/ \
    --changes \
    --vcf \
    --diploid \
    --vcfqe \
    --tracks