Excessive memory usage with the polish option
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tomasbruna commented
Thanks for the excellent tool! When running Liftoff between tomato genomes (~800 Mbp, 35k genes) with the following command:
liftoff Slycopersicum_691_SL4.0.fa Slycopersicum_390_v2.5.fa -g Slycopersicum_390_ITAG2.4.gene_exons.gff3 -o lifted.gff3 -p 32 -polish
it starts consuming a lot of memory and eventually crashes when the memory usage exceeds 100 Gb. Stderr log is here: liftoff_stderr.txt
To reproduce, you can download the input files from JGI's Data Portal at https://data.jgi.doe.gov/refine-download/phytozome?organism=Slycopersicum&expanded=Phytozome-390%2CPhytozome-691. I'm getting the error with the latest Liftoff (v1.6.3) and minimap2 (v2.24-r1122) releases.
Everything works fine without the -polish option, so this is not a pressing issue. Just wanted to make a record of this.
Best,
Tomas