I've had the equivalent of the following code in pytaxonkit's test suite for a while now.
echo -e "131567\n2\n1224\n1236\n91347\n543\n561\n562\n2605619\n10239\n2731341\n2731360\n2731618\n2731619\n28883\n10699\n196894\n1327037\n" \
| taxonkit filter --threads 1 --equal-to species --lower-than species --save-predictable-norank
In recent weeks this test started causing CI failures—the command would just hang for hours. Only today have I had a chance to track down the issue. After a bit of trial and error, I discovered (with the taxonkit lineage command) that a few of these taxids had been merged.
Prerequisites
taxonkit version
Describe your issue
I've had the equivalent of the following code in pytaxonkit's test suite for a while now.
In recent weeks this test started causing CI failures—the command would just hang for hours. Only today have I had a chance to track down the issue. After a bit of trial and error, I discovered (with the
taxonkit lineage
command) that a few of these taxids had been merged.When I dropped or replaced the merged taxids, the problem went away and I got the expected answer.
Can you confirm that
taxonkit filter
is choking on merged taxids here?