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Hi, professor fasnicar
Now i have a question about the option -g in phylophlan_get_reference.
I downloaded ref genomes for genus Acinetobacter by this command (phylophlan_get_reference -g g__Acinetobacter -o input_genomes/ -n 1 --verbose 2>&1 | tee logs/phylophlan_get_reference.log). And i got 227 genomes of this genus finally. The txt(assembly_summary_genbank.txt) shows that over 10,000 species belong to genus Acinetobacter. And then I tried other command (-n 300), but i got 806 genomes finally.
On what basis were these 227 or 806 species selected? And did they include all child taxa (species) with a validly published of the genus?
Thanks
The text was updated successfully, but these errors were encountered:
then up to 5 genomes for each species listed under g__Acinetobacter will be downloaded.
Now, again for the sake of the example, assume that there are only 3 species followed by the number of available genomes:
The above means that there are 227 species listed under g__Acinetobacter and in total there are 2984 genomes that can be retrieved. So, it makes sense that you downloaded 227 genomes with -n 1 and 806 with -n 300
As there is s__Acinetobacter_baumannii with 2478 genomes.
Hi, professor fasnicar
Now i have a question about the option -g in phylophlan_get_reference.
I downloaded ref genomes for genus Acinetobacter by this command (phylophlan_get_reference -g g__Acinetobacter -o input_genomes/ -n 1 --verbose 2>&1 | tee logs/phylophlan_get_reference.log). And i got 227 genomes of this genus finally. The txt(assembly_summary_genbank.txt) shows that over 10,000 species belong to genus Acinetobacter. And then I tried other command (-n 300), but i got 806 genomes finally.
On what basis were these 227 or 806 species selected? And did they include all child taxa (species) with a validly published of the genus?
Thanks
The text was updated successfully, but these errors were encountered: