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Error while running metagenomesimulation.py: "Invalid taxID: ' ' " #103
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That looks like a taxonomy ID in your |
Sure - I've attached it here. it is quite long because I've input a lot of genomes. |
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 |
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? |
Oh, sure, just send it to adrian.fritz at helmholtz-hzi.de |
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 |
I have tested that CAMISIM can handle with missing ranks now . Thanks ! |
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
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