Funannotate is a genome prediction, annotation, and comparison software package. It was originally written to annotate fungal genomes (small eukaryotes ~ 30 Mb genomes), but has evolved over time to accomodate larger genomes.
[user@biowulf]$ sinteractive --gres=lscratch:10 --mem=10g -c4 [user@cn4279 ~]$ module load funannotate [+] Loading bamtools 2.5.2 on cn4279 [+] Loading singularity 4.1.5 on cn4279 [+] Loading bedtools 2.31.1 [+] Loading blast 2.15.0+ ... [+] Loading eggnog-mapper 2.1.6 [+] Loading exonerate, version 2.4.0... [+] Loading hmmer 3.3.2 on cn4279 [+] Loading hisat2 2.2.1 on cn4279 [+] Loading samtools 1.21 ... [+] Loading kallisto, version 0.51.1... [+] Loading Mafft 7.526 ... [+] Loading minimap2, version 2.28... [+] Loading mysql 8.0.34 on cn4279 [+] Loading gcc 8.5.0 ... [+] Loading repeatmasker 4.1.7-p1 on cn4279 [+] Loading salmon 1.10.1 [+] Loading signalp 6.0g ... [+] Loading stringtie 2.2.3 [+] Loading Trinity 2.15.1 ... [+] Loading tantan 40 [+] Loading trnascan-se 2.0.9 on cn4279 [+] Loading trimal 1.2rev59 [+] Loading trimmomatic 0.39 on cn4279 [+] Loading ucsc 472 on cn4279 [+] Loading funannotate 1.8.17 on cn4279The funannotate data processing pipeline involves several core modules:
[user@cn4279 ~]$ funannotate -h Usage: funannotate <command> <arguments> version: 1.8.17 Description: Funannotate is a genome prediction, annotation, and comparison pipeline. Commands: clean Find/remove small repetitive contigs sort Sort by size and rename contig headers mask Repeatmask genome assembly train RNA-seq mediated training of Augustus/GeneMark predict Run gene prediction pipeline fix Fix annotation errors (generate new GenBank file) update RNA-seq/PASA mediated gene model refinement remote Partial functional annotation using remote servers iprscan InterProScan5 search (Docker or local) annotate Assign functional annotation to gene predictions compare Compare funannotated genomes util Format conversion and misc utilities setup Setup/Install databases test Download/Run funannotate installation tests check Check Python, Perl, and External dependencies [--show-versions] species list pre-trained Augustus species database Manage databases outgroups Manage outgroups for funannotate compareThese modules are supposed to be used in the following order:
[user@cn4279 ~] cp /usr/local/apps/funannotate/1.8.17/GeneMark/gm_key_64 ~/.gm_keyNow proceed with setting up:
[user@biowulf]$ funannotate setup -h
Usage: funannotate clean <arguments>
version: 1.8.17
Description: The script sorts contigs by size, starting with shortest contigs it uses minimap2
to find contigs duplicated elsewhere, and then removes duplicated contigs.
Arguments:
-i, --input Multi-fasta genome file (Required)
-o, --out Cleaned multi-fasta output file (Required)
-p, --pident Percent identity of overlap. Default = 95
-c, --cov Percent coverage of overlap. Default = 95
-m, --minlen Minimum length of contig to keep. Default = 500
--exhaustive Test every contig. Default is to stop at N50 value.
[user@biowulf]$ funannotate setup -i pfam -d ./databases --force
-------------------------------------------------------
[Aug 15 07:50 PM]: OS: Debian GNU/Linux 10, 56 cores, ~ 264 GB RAM. Python: 3.8.13
[Aug 15 07:50 PM]: Running 1.8.13
[Aug 15 07:50 PM]: Database location: ./databases
[Aug 15 07:50 PM]: Retrieving download links from GitHub Repo
[Aug 15 07:50 PM]: Parsing Augustus pre-trained species and porting to funannotate
[Aug 15 07:50 PM]: Downloading UniProtKB/SwissProt database
[Aug 15 07:50 PM]: Downloading: http://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz Bytes: 91192930
[Aug 15 07:50 PM]: Downloading: http://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/reldate.txt Bytes: 151
[Aug 15 07:50 PM]: Building diamond database
[Aug 15 07:50 PM]: UniProtKB Database: version=2022_03 date=2022-08-03 records=568,002
[Aug 15 07:50 PM]: Funannoate setup complete. Add this to ~/.bash_profile or ~/.bash_aliases:
export FUNANNOTATE_DB=/gpfs/gsfs7/users/user/funannotate/databases
[user@biowulf]$ funannotate sort -h
Usage: funannotate sort <arguments>
version: 1.8.17
Description: Script will download/format necessary databases for funannotate.
Options:
-i, --install Download format databases. Default: all
[merops,uniprot,dbCAN,pfam,repeats,go,
mibig,interpro,busco_outgroups,gene2product]
-b, --busco_db Busco Databases to install. Default: dikarya [all,fungi,aves,etc]
-d, --database Path to funannotate database
-u, --update Check remote md5 and update if newer version found
-f, --force Force overwriting database
-w, --wget Use wget to download instead of python requests
-l, --local Use local resource JSON file instead of current on github
[user@biowulf]$ funannotate -i pfam
[Aug 15 01:23 PM]: OS: CentOS Linux 7, 56 cores, ~ 264 GB RAM. Python: 3.7.11
[Aug 15 01:23 PM]: Running 1.8.17
[Aug 15 01:23 PM]: Database location: /fdb/funannotate/db
[Aug 15 01:23 PM]: Retrieving download links from GitHub Repo
[Aug 15 01:23 PM]: Parsing Augustus pre-trained species and porting to funannotate
[Aug 15 01:23 PM]: Pfam Database: version=34.0 date=2021-03 records=19,179
[user@biowulf]$ funannotate mask -h
Usage: funannotate mask <arguments>
version: 1.8.17
Description: This script is a wrapper for repeat masking. Default is to run very simple
repeat masking with tantan. The script can also run RepeatMasker and/or
RepeatModeler. It will generate a softmasked genome. Tantan is probably not
sufficient for soft-masking an assembly, but with RepBase no longer being
available RepeatMasker/Modeler may not be functional for many users.
Arguments:
-i, --input Multi-FASTA genome file. (Required)
-o, --out Output softmasked FASTA file. (Required)
Optional:
-m, --method Method to use. Default: tantan [repeatmasker, repeatmodeler]
-s, --repeatmasker_species Species to use for RepeatMasker
-l, --repeatmodeler_lib Custom repeat database (FASTA format)
--cpus Number of cpus to use. Default: 2
--debug Keep intermediate files
etc.
[user@cn4279 ~]$ exit salloc.exe: Relinquishing job allocation 46116226