lambda3 complains that the pre-built uniref50 index does not contain a taxonomic tree

[uludag]

I was trying to run lambda3 with the pre-built uniref50 database, lambda3 complains that the index does not contain a taxonomic tree:

$ lambda3 searchp -q ../query.fasta -i ./uniref50_20230713.lba.gz --output-columns 'std lcaid lcataxid'
LAMBDA - the Local Aligner for Massive Biological DatA
======================================================
Version 3.0.0

Reading index properties... done.
Detecting query alphabet... aminoacid detected.
Checking memory requirements... met.
Loading Database Index... done.


ERROR: The following unspecified exception was thrown:
       "You requested taxonomic binning, but the index does not contain a taxonomic tree. Recreate it and provide --tax-dump-dir ."
       If the problem persists, report an issue at https://github.com/seqan/lambda/issues and include this output, as well as the output of `lambda3 --version`, thanks!

Thanks for making Lambda and for supporting its users
--mahmut

[h-2]

Yes, if you want lcaid and lcataxid, you need to add taxonomic information (as the error message says). See also https://github.com/seqan/lambda/wiki/Taxonomic-Workflows for more information!

[uludag]

Thanks, but I'm confused, the log file of the index suggests that the index was built with taxonomic information

Parsing acc-to-tax-map file... done.
Runtime: 438.245s
Subjects without tax IDs: 9510326/60952894
Subjects with more than one tax ID: 0/60952894

Parsing nodes.dmp... done.
Runtime: 0.282s
Number of nodes in tree: 2509792
Maximum Tree Height: 36

Thinning and flattening Tree... done.
Runtime: 0.03s
Number of nodes in tree: 150443
Maximum Tree Height: 35

Is it possible that the tree is included in the index but for some reason lamda3 is not able to find it?
--mahmut

[sarahet]

Yes, you are right that it should be there. We will look into this, thanks for reporting it!

[sarahet]

This has been fixed by #227. You should be able to run the search with the most recent version of the lambda3 branch.

[uludag]

Thanks @h-2 @sarahet I don't get the missing tree error any more; my test search with the lca options, with the pre-built uniref50 index completed without error.