Error while running metagenomesimulation.py: "Invalid taxID: ' ' "

[IsaacT1123]

I'm using the python2.7 version of CAMISIM, and I'm getting the following error while running metagenomesimulation.py:

2021-03-22 14:44:09 INFO: [MetagenomeSimulationPipeline] Metagenome simulation starting 2021-03-22 14:44:09 INFO: [MetagenomeSimulationPipeline] Validating Genomes 2021-03-22 14:44:09 INFO: [MetadataReader] Reading file: '[MY PARENT DIRECTORY]/CAMISIM/defaults/new_genome_to_id.tsv' 2021-03-22 14:46:58 INFO: [MetadataReader 9216059885] Reading file: '[MY PARENT DIRECTORY]/CAMISIM/defaults/new_metadata.tsv' 2021-03-22 14:46:58 INFO: [MetadataReader 82380310288] Reading file: '[MY PARENT DIRECTORY]/CAMISIM/out/internal/genome_locations.tsv' 2021-03-22 14:46:59 INFO: [NcbiTaxonomy] Building taxonomy tree... 2021-03-22 14:46:59 INFO: [NcbiTaxonomy] Reading 'nodes' file: '/tmp/tmpzCnYL8/NCBI/nodes.dmp' 2021-03-22 14:47:19 INFO: [NcbiTaxonomy] Reading 'names' file: '/tmp/tmpzCnYL8/NCBI/names.dmp' 2021-03-22 14:47:22 INFO: [NcbiTaxonomy] Reading 'merged' file: '/tmp/tmpzCnYL8/NCBI/merged.dmp' 2021-03-22 14:47:23 INFO: [NcbiTaxonomy] Done (23.0s) 2021-03-22 14:47:23 ERROR: [NcbiTaxonomy] Invalid taxid: '' 2021-03-22 14:47:23 ERROR: [MetagenomeSimulationPipeline] Invalid taxid in line 80 2021-03-22 14:47:23 INFO: [MetagenomeSimulationPipeline] Metagenome simulation aborted

I've deliberately input genomes that are present in the taxdump that CAMISIM is using, so I find this issue quite confusing.
I've attached my config file as well.

Thanks for your help!

new_miniconfig.txt

[AlphaSquad]

That looks like a taxonomy ID in your metadata.tsv file isn't set, could you maybe also check/send this file?

[IsaacT1123]

Sure - I've attached it here. it is quite long because I've input a lot of genomes.

new_metadata.txt

[AlphaSquad]

Hm, I cannot immediately see something wrong with this. I see that you added a different taxonomy version to your config file. Does your taxonomy have the same structure as the provided taxonomy tarballs? In particular, it needs a head directory called NCBI and then the .dmp files below that (at least names.dmp, nodes.dmp, merged.dmp). If that is already the case, then I would also need you tax dump to be able to reproduce - I am sorry that it is such a hassle.

[IsaacT1123]

No worries - the taxonomy dump is too big to attach here, but I could email it to you instead - what's a good email address I could send this to?
Thanks!

[AlphaSquad]

Oh, sure, just send it to adrian.fritz at helmholtz-hzi.de

[AlphaSquad]

Alright, I took a deeper dive to find out what's going on and the problem is that there is a few genomes which do not have a complete lineage, e.g. genome75 from your file is Victivallales bacterium CCUG 44730 and does not have a family tax ID in the NCBI, because it is a unclassified Victivallales.
I added a check for missing ranks now, so the simulation should work again and print a warning in the log. The taxonomic profiles will miss these specific genomes at these ranks then, it becomes possible that more sequences are classified at a lower level than at a higher level in the profil, i.e. the Victivallales bacterium species has some abundance, but not its family (since there is none).

[manli-zou]

I have tested that CAMISIM can handle with missing ranks now . Thanks !