mapping on nanopore data Error: killed

lh3 / minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

https://lh3.github.io/minimap2

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mapping on nanopore data Error: killed #338

Closed shashibioinfo closed 5 years ago

shashibioinfo commented 5 years ago

we have Nanopore metagenome data from MinION platforms which was mapped to Nucleotide sequence database(nt.gz) using minimap2 tool on 15GB RAM and after few minutes the process stops with error message "Killed". even after trying multiple times.

minimap2 -ax map-ont nt.fa /home/ubuntu/Leucine_rawdata/barcode3_5.fastq > barcode3_5_aligned.sam

If you can please help us to resolve this issue.

Thank you

lh3 commented 5 years ago

15GB is not enough. Better find a machine with more RAM. You can reduce -I to -I2g, but on nt, it will be slow.