No assignments using SEED and EggNog mapping file. Database problem?

User Questions
1

Hello

I am trying to assign reads to functional categories using SEED and EggNog and used the approach described here, but with the ncbi env_nr instead of the nr database:
http://megan.informatik.uni-tuebingen.de/t/generic-pipeline-using-diamond-and-megan6/50

290 hits are found, but they are classified as “not assigned” in MEGAN, so I guess I am doing something wrong.
The commands I use:

#Make database
diamond makedb --in env_nr.gz -p 10 -d eggnog

#Blast
diamond blastx --query 00fastq/TestSample.fasta --db eggnog --daa 10daa/reads.daa

#Daa2rma
daa2rma -i 10daa/reads.daa -o 20rma/reads.rma --acc2eggnog acc2eggnog-Oct2016X.abin

Or

#Daa-Meganizer
daa-meganizer -i 10daa/reads.daa -a2eggnog acc2eggnog-Oct2016X.abin

Both givethe same result:

Total reads: 290
With hits: 290
Alignments: 3,447
Assig. Taxonomy: 0
Assig. EGGNOG: 0
MinSupport set to: 1
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% (0.3s)
Min-supp. changes: 0
10% 20% 100% (0.1s)
Class. Taxonomy: 1
Class. EGGNOG: 1

Am I using a wrong command, or is that a env-nr database problem?

Thank you
Jan

2

I’ve never used env_nr.gz… What do the entries look like, please send me the first 100 lines and I will determine whether it is a mapping file problem

3

Hello! Where did you find env_nr.gz? If you download the env_nr database from the BLAST website, it gives you 3 separate env_nr.tar.gz files with a bunch of different format files inside. Diamond needs a single .fa file to makedb, but env_nr doesn’t come like that. Any idea how to use env_nr with diamond? I tried some stuff from here https://www.uppmax.uu.se/resources/databases/diamond-protein-alignment-databases/ but it doesn’t work. Thanks!

4

Please post this question on the Diamond GitHub webpage.