How to use docker tool eggnog to annotate

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Using the docker tool eggnog to annotate, take Arabidopsis thaliana as an example:

# GO KEGG annotations and enrichment analysis of non-model species # decompression after downloading eggnog database Put it in a directory # start the image # docker run-- rm-- cpus 8-m 16G-it-v / share/nas1/huangls/test/eggnog:/work-v / share/work/database/eggNOG/emapperdb-5.0.2/:/database / eggnog:latest# a gene extract a pep representative sequence # python scripts/get_gene_fa.py-- gff Arabidopsis_thaliana.TAIR10.31.gff3\ #-f Arabidopsis_thaliana.TAIR10.31.pep Batch annotation of .all.fa-p pep# protein sequence emapper.py-I pep.fa-o pep-m diamond-- cpu 8-- seed_ortholog_evalue 1e-5-- override\-- dmnd_db / database/eggnog_proteins.dmnd-- data_dir / database/

-m specifies the diamond method, which defaults to the hmmer method. Diamond only shows speed advantage when there are more than a thousand sequences, a small number of sequences will feel very slow, and the results are not as accurate as hmmer, especially for remote source annotations.

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