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bbuchfink / diamond

Accelerated BLAST compatible local sequence aligner.
GNU General Public License v3.0
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Protein alignment an taxonomic binning with DIAMOND v2.0.15 and Megan #643

Open alicaheid opened 1 year ago

alicaheid commented 1 year ago

Hi, I'm using DIAMOND v2.0.15 to perform a Protein alignment against the NCBI-nr database and a subsequent taxonomic binning with Megan. I formed the DIAMOND index with

diamond makedb --in nr.gz -d nr

Then I run DIAMOND on a fasta file with

diamond blastx -d nr.dmnd -q reads.fa -fast -o reads.daa -f 0 -k 20

Then I tried to Run Megan on my DIAMOND output file

MEGAN/tools/daa-meganizer -i reads.daa -mdb megan-map.db

but it did not work

Then I tried to put my diamond output into Megan to get a taxonomic Tree but none could be displayed. Of course I made sure that the diamond output and the corresponding FASTA file are in the same folder and have the same name.

Is there a setting somewhere I've missed? Thank you in advance for your help.

bbuchfink commented 1 year ago

This sounds like a problem with megan, please ask your question here: https://megan.cs.uni-tuebingen.de/

ko519 commented 1 year ago

Hi, possible that you should be using -f 100 instead of 0...

"-f 100 DIAMOND alignment archive (DAA). The DAA format is a proprietary binary format that can subsequently be used to generate other output formats using the view command. It is also supported by MEGAN and allows a quick import of results. Note that this format does not support streaming output or taxonomy features. It is considered a legacy format at this time."

katievigil commented 1 year ago

@ko519 where you able to meganize your DAA file?