shenwei356
commented
7 months ago NCBI taxonomy updates frequently, some taxids might be deleted. So, what's the version of your taxdump files, when did you download them?
I've just tested with the newly downloaded files.
$ (echo 3084967; echo 238) | taxonkit lineage | csvtk pretty -Ht -W 60 -x ';'
3084967 cellular organisms;Bacteria;Pseudomonadota;
Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;
Pseudomonas;unclassified Pseudomonas;
Pseudomonas sp. FRB 230
238 cellular organisms;Bacteria;FCB group;
Bacteroidota/Chlorobiota group;Bacteroidota;Flavobacteriia;
Flavobacteriales;Weeksellaceae;Elizabethkingia;
Elizabethkingia meningoseptica For the result of taxid 238 you mentioned above, it's strange because there have been no big changes to taxid 238 during the last 9 years, according to the taxid-changelog.
238 Elizabethkingia;Elizabethkingia meningoseptica$ zcat taxid-changelog.csv.gz | csvtk grep -f taxid -p 238 | csvtk cut -f 1-3,5-7 | csvtk pretty -W 40 -x ';'
taxid version change name rank lineage
----- ---------- -------------- ------------------------------ ------- ----------------------------------------
238 2014-08-01 NEW Elizabethkingia meningoseptica species cellular organisms;Bacteria;
Bacteroidetes/Chlorobi group;
Bacteroidetes;Flavobacteriia;
Flavobacteriales;Flavobacteriaceae;
Elizabethkingia;
Elizabethkingia meningoseptica
238 2016-03-01 CHANGE_LIN_LEN Elizabethkingia meningoseptica species cellular organisms;Bacteria;FCB group;
Bacteroidetes/Chlorobi group;
Bacteroidetes;Flavobacteriia;
Flavobacteriales;Flavobacteriaceae;
Elizabethkingia;
Elizabethkingia meningoseptica
238 2020-09-01 CHANGE_LIN_TAX Elizabethkingia meningoseptica species cellular organisms;Bacteria;FCB group;
Bacteroidetes/Chlorobi group;
Bacteroidetes;Flavobacteriia;
Flavobacteriales;Weeksellaceae;
Elizabethkingia;
Elizabethkingia meningoseptica
238 2022-10-01 CHANGE_LIN_LIN Elizabethkingia meningoseptica species cellular organisms;Bacteria;FCB group;
Bacteroidetes/Chlorobi group;
Bacteroidota;Flavobacteriia;
Flavobacteriales;Weeksellaceae;
Elizabethkingia;
Elizabethkingia meningoseptica
238 2023-05-01 CHANGE_LIN_LIN Elizabethkingia meningoseptica species cellular organisms;Bacteria;FCB group;
Bacteroidota/Chlorobiota group;
Bacteroidota;Flavobacteriia;
Flavobacteriales;Weeksellaceae;
Elizabethkingia;
Elizabethkingia meningoseptica
some taxid that have taxonomy on NCBI but taxonkit not found or not complete taxonkit v0.15.1
taxonkit lineage 0.txt|less : 20:24:21.750 [WARN] taxid 3046382 not found 20:24:21.751 [WARN] taxid 3046383 not found 20:24:21.751 [WARN] taxid 3051092 was deleted 20:24:21.751 [WARN] taxid 3051103 was deleted 20:24:21.751 [WARN] taxid 3051154 was deleted 20:24:21.751 [WARN] taxid 3051614 was deleted 20:24:21.751 [WARN] taxid 3051890 was deleted 20:24:21.751 [WARN] taxid 3063952 not found 20:24:21.751 [WARN] taxid 3064195 not found 20:24:21.751 [WARN] taxid 3084967 not found 238 Elizabethkingia;Elizabethkingia meningoseptica
However, the ncbi taxonomy is : Taxonomy ID: 3084967 (for references in articles please use NCBI:txid3084967) Lineage( full ) cellular organisms; Bacteria; Pseudomonadota; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Pseudomonas; unclassified Pseudomonas
Taxonomy ID: 238 Lineage (full): cellular organisms; Bacteria; FCB group; Bacteroidota/Chlorobiota group; Bacteroidota; Flavobacteriia; Flavobacteriales; Weeksellaceae; Elizabethkingia
In my tax-id file, many classification ids are in this situation. How should I solve this problem?
Looking forward to your reply!