I need to create a local BLASTN db containing the fasta RefSeq sequences of viruses. I would like to download the fasta sequences from https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus using the browser, but it takes too long time and the connection fails (I am in China). I also tried to use the ncbi-genome-download application (ncbi-genome-download --formats fasta viral), but it is still running after 24h. Please, can someone help me? Any suggestions? Thank you very much
You may be tempted to use more than 12 threads. I caution you not to do it, even if you have more threads available. What will happen is that NCBI will throttle down your connections if your IP number tries to download too many files in a small period of time. Sometimes using 10 threads will get the job done sooner than using 20.