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taxonkit lineage stalls if taxID = 1 #7

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nick-youngblut opened this issue Jan 4, 2018 · 1 comment
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taxonkit lineage stalls if taxID = 1 #7

nick-youngblut opened this issue Jan 4, 2018 · 1 comment
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@nick-youngblut
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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 shenwei356 added the bug label Jan 4, 2018
shenwei356 added a commit that referenced this issue Jan 4, 2018
@shenwei356
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fixed in v0.2.4-dev2

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