... These are lots of factors affecting the computation time:
- BLAST database size. e.g., NCBI NR is very very big.
- Query sequences size.
- `-num_threads`. *You did not set `-num_threads`, which defines number of CPUs to use. I think this the main cause for your case.*
- Computer ...
... [I just counted the bacterial species with complete genomes](http://blog.shenwei.me/manipulation-on-ncbi-refseq-bacterial-assembly-summary/) according to the ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt , it's `2517`.
$ cat assembly_summary.txt | grep "Complete Genom ...
... Using [csvtk](https://github.com/shenwei356/csvtk) or csvkit, or miller or xsv.... csvtk is a cross-platform, efficient, practical and pretty CSV/TSV toolkit in Golang. Hope you enjoy it.
For a CSV file:
$ cat 3.csv
... For Linux/Mac OS X, using shell command `sed` is the simplest way:
# by removing "|" and later characters:
sed -r 's/\|.+//' seqs.fa > newseqs.fa
Since you asked `sed` command, please ignore method below:
If you need to run on Windows, the simplest way is using [seqkit](http://bioinf ...