search

wejlab / MetaScope

An R-based approach for preprocessing and aligning 16S, metagenomic, and metatranscriptomic data (PathoScope version 3.0)
GNU General Public License v3.0
16 stars 7 forks source link

No available genome for bacteria - object 'combined_fasta' not found #9

Closed tyden46 closed 3 years ago

tyden46 commented 3 years ago

Hi, I installed Metascope on April 8, 2021 and I am trying to download all of the refseq bacterial genomes using the download_refseq() function. I am running download_refseq('bacteria', reference = TRUE, representative = TRUE) but I am getting the following error on R4.0.3:

No available genome for bacteria - try setting both representative and reference to TRUE Error in download_refseq("bacteria", reference = TRUE, representative = TRUE) : object 'combined_fasta' not found Execution halted

I have also tried setting representative to FALSE and not including the representative flag at all. Using a capital "B" to write "Bacteria" as an argument to download_refseq() works but gives me only 7 genomes.

aubreyodom commented 3 years ago

Hi, the issue should be fixed, although the package is still very much under development at the moment as we are working to transition to the bowtie2 aligner. Use at your own risk :)