I am new to Diamond and I have two questions.
I ran the makedb command to set up the reference database without any error message and got the nr.dmnd file. Then I tried to aligned my sample back and I ran this following commands and got error message.
$ diamond blastx -d nr -q R1.paired.fq -o matches.m8
Error: Missing parameter: DAA file (--daa/-a)
I am confused because the DAA file should not be required at this step according to their manual.
My data are shot gun metagenomics data and the paired end reads won't overlap and I can not merge them. In my case, shall I just either use R1 or R2 as input or is it better that I join R1&R2 into one file even if they won't merge?
Thanks for help!