Diamond blastx error: Missing parameter: DAA file (--daa/-a)

Question

[wintergb]

I am new to Diamond and I have two questions.

1. 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.

2. 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!

[GenoMax]

R1 or R2 should give you very similar answer (unless you have some chimeric reads) so using either file should be fine.

Answer 1

[Steven Lakin]

I believe in earlier versions, diamond required an intermediate DAA format, which you would then parse with the diamond view command. However, it seems now that it has been updated to allow direct output to BLAST tabular. You might try specifying the -f tab option explicitly, or compare your version to theirs to make sure that you're up to date with the documentation.

Alternatively, you could specify the -a option and then parse it like so:

diamond blastx -d nr -q R1.paired.fq -a matches.daa
diamond view -a matches.daa -f tab -o OUTPUT_FILE