I'm using taxonkit v0.2.0 (installed via bioconda), and I was running taxonkit lineage on the "hits" file generated by centrifuge. taxonkit lineage would very quickly write out taxonomies for the first ~60000 hits, but then stall and the memory used would climb to >300 GB. It turns out that one of the centrifuge hits had a taxID of "1" (centifuge called this a "no rank"). I filtered out this "no rank" hits, which fixed this stalling issue.
shenwei356
commented
6 years ago
I'm using
taxonkitv0.2.0 (installed via bioconda), and I was runningtaxonkit lineageon the "hits" file generated bycentrifuge.taxonkit lineagewould very quickly write out taxonomies for the first ~60000 hits, but then stall and the memory used would climb to >300 GB. It turns out that one of the centrifuge hits had a taxID of "1" (centifuge called this a "no rank"). I filtered out this "no rank" hits, which fixed this stalling issue.