Expected runtime?


New member

I m running Diamond for a set of 23 unknown contigs with an average length of 36376 bp. My program has been running for >1 hour. What is the expected total runtime for this run?

The command I used is: diamond blastx --query <contigs> -v -d diamonddb/nr.dmnd -o ../CGT3027_diamond

I am running this program on a server with 44 cores.

Benjamin Buchfink

Staff member
This may take a couple of hours against the NR as Diamond is not that efficient when the number of queries is small. When aligning contigs it would be useful to use the --long-reads option.

If your server has a lot of memory, a good way to speed it up is to use a higher block size like this: -b6 -c1. You can also use higher numbers for -b depending on your memory.