Warning: Taxon ID is not contained in nodes.dmp.

[Tamtatatam]

Hi

I have several files from the kaiju webserver and I would like to combine them using kaiju2table.

However, I get dozens of warnings ("Warning: Taxon ID XY is not contained in nodes.dmp."). I tried using the latest nodes.dmp and names.dmp, and also downloaded older versions from NCBI as the webserver uses older databases, but that did not help.

Is that a known and expected problem, or am I using the wrong files? If so, which version should I use?

Thanks!

[pmenzel]

Hi

try to download and unpack the file http://kaiju.binf.ku.dk/database/kaiju_index.tgz
and use these nodes and names dmp files, which are the one used by the web server.

[palc]

I see a similar issue and error message of hundreds of lines

Warning: Taxon ID 2171752 is not contained in nodes.dmp.
Warning: Taxon ID 1940818 is not contained in nodes.dmp.
Warning: Taxon ID 2171752 is not contained in nodes.dmp.

I downloaded the kaiju_db_nr_euk.fmi etc. file from Kajiju in March and ran the kaiju via command line last month. I tried both taxdump versions from March and July when combining kaiju.out tables but still same issues.

[pmenzel]

This happens when taxonomy IDs are replaces by new IDs, but the old ones are still used in the nr database, you can see that in the merged.dmp file from taxdump.tar.gz:

$ grep 1940818 merged.dmp
1940818 |       2548426 |

$ grep 2171752 merged.dmp
2171752 |       2080658 |

So, 1940818 was replaced with 2548426 and 2171752 with 2080658.
If it is just these two IDs in, then you could simply replace them manually.

[astromicronaut]

I also have files from the kaiju webserver and I would like to combine them using kaiju2table, but trying with all the options I cant really merge, kaiju2table only paste the results in rows in the same file repiting taxons and creating a big file. What I need is create a file that unifique taxons and just add columns for each sample. Could anyone help me? please