Taxonomy Parse errors

[chiras]

[01-15 14:10:34] [ReferenceDbCreator] Adding taxonomy to fasta Use of uninitialized value in numeric eq (==) at /NCBI-Taxonomy/lib/NCBI/Taxonomy.pm line 407, <IN> line 157.
Happens for approx 30 IDs after downloading seqs and taxfile with the command specified in #14

[iimog]

I'll have to dig into this. Will do it asap (probably tonight).

[iimog]

I finally got around to digging into this problem. Apparently these messages indicate that for some taxid the lineage could not be found in the local nodes.dmp and names.dmp. In consequence the tax= field in the fasta file remains empty. A similar message is printed by Krona in the end:

   [ WARNING ]  The following taxonomy IDs were not found in the local
                database and were set to root (if they were recently added to                                                                 
                NCBI, use updateTaxonomy.sh to update the local database):                                                                    
                2486830 2338477 2338481 2486579 2338462 2338482 2338485 2338470
...

So it is required to update the local taxonomy dumps inside the docker containers:

cd /NCBI-Taxonomy/
perl make_taxid_indizes.pl
cd /Krona/KronaTools/
./updateTaxonomy.sh

Running the same command afterwards produces no warnings. Those commands do not take very long but it is still not necessarily the best option to run them every time a reference database is created. Every time the docker image is built (beware of caching) the taxonomy databases are updated. However, this is probably too rare. We should probably include some script to do this automatically or a cron job (at least for the web interface).