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bokulich-lab / RESCRIPt

REference Sequence annotation and CuRatIon Pipeline
BSD 3-Clause "New" or "Revised" License
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get-ncbi-data Command Error #185

Closed rachelhawrit closed 4 months ago

rachelhawrit commented 4 months ago

I am getting the following error when running the get-ncbi-data This occurs even if I rearrange the order of parameters and outputs, and by changing the query to be enclosed with "" instead of ''. There are no spaces in my code either. I am trying to obtain the ncbi 16S database to be used for Blast consensus classification!

module load anaconda3 conda activate qiime2-amplicon-2024.2

qiime rescript get-ncbi-data --o-sequences ncbi-seq.qza \ --o-taxonomy ncbis-tax.qza \ --p-n-jobs 28 \ --p-query '(16s[All Fields] AND rrna[All Fields] AND sequence[All Fields]) AND bacteria[filter]' \ --verbose

              There were some problems with the command:

(1/2) Missing option '--o-sequences'. ("--output-dir" may also be used) (2/2) Missing option '--o-taxonomy'. ("--output-dir" may also be used) /var/spool/slurm/slurmd/job8407554/slurm_script: line 13: --o-sequences: command not found

nbokulich commented 4 months ago

Hi @rachelhawrit , Thank you for using RESCRIPt. All tech support and user questions are handled on the QIIME 2 forum, not on the RESCRIPt issue tracker, so please re-post your questions on the forum and we can help you there. Thanks!