Traceback (most recent call last):
File "/home/bmlab/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/commands.py", line 329, in call
results = action(**arguments)
File "", line 2, in get_ncbi_data
File "/home/bmlab/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
File "/home/bmlab/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/sdk/action.py", line 390, in callable_executor
output_views = self._callable(**view_args)
File "/home/bmlab/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/rescript/ncbi.py", line 82, in get_ncbi_data
taxids, ranks, rank_propagation, entrez_delay)
File "/home/bmlab/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/rescript/ncbi.py", line 255, in get_taxonomies
AttributeError: 'dict' object has no attribute 'add'
Plugin error from rescript:
'dict' object has no attribute 'add'
See above for debug info.
Isn't the tool supposed to get data from any BioProject just as 16S? I want to build a database for ITS region. Could you point me to the reason of this failure?
Edit: Well... The command below is not working for me either.
I’ve tried running these commands, and initially I ran into the same errors too. However, I adjusted the --p-entrez-delay by doubling the default value, and it worked. This leads me to think that the issue in on the NCBI-end.
The following worked (with and without the --p-n-jobs argument):
qiime rescript get-ncbi-data \
--p-query '33175[BioProject] OR 33317[BioProject]' \
--o-sequences ncbi-refseqs-unfiltered.qza. \
--o-taxonomy ncbi-refseqs-taxonomy-unfiltered.qza \
--p-entrez-delay 0.668 \
Saved FeatureData[Sequence] to: ncbi-refseqs-unfiltered.qza
Saved FeatureData[Taxonomy] to: ncbi-refseqs-taxonomy-unfiltered.qza
There is no --p-n-jobs argument. I use the version stated below. Is there another version that has --p-n-jobs argument?
QIIME 2 Plugin ‘rescript’ version 2020.11.0.dev0+6.g836422d (from package ‘rescript’ version 2020.11.0.dev0+6.g836422d)
Time zone difference corresponds to 10 hours for USA and my country, so my active hours should be somewhat quiet and still it fails. The weird thing is, error message differs for each attempt. I can send error logs if it matters.
I will build database from this BioProject some other way and try rescript after updates. I will let you know how that goes if anyone is interested.