# Funannotate 1.8.7


## funannotate

funannotate is a pipeline for genome annotation (built specifically for fungi,
but will also work with higher eukaryotes). Installation, usage, and more
information can be found at <http://funannotate.readthedocs.io>

To activate, check out a node with `qrsh` and run:

```console
bash
source /local/cluster/funannotate/activate.sh
```

To use in SGE_Batch, write a shell script that includes the above source line,
then the commands you would like to run.

Location and version:

```console
(/local/cluster/funannotate-1.8.7) [Linux@chrom1 ~]$ which funannotate
/local/cluster/funannotate-1.8.7/bin/funannotate
(/local/cluster/funannotate-1.8.7) [Linux@chrom1 ~]$ funannotate --version
funannotate v1.8.7
```

DB Path:

```console
$FUNANNOTATE_DB=/nfs1/CGRB/databases/funannotate/current
```

help message:

```console
$ funannotate --help

Usage:       funannotate <command> <arguments>
version:     1.8.7

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 compare

Written by Jon Palmer (2016-2019) nextgenusfs@gmail.com
```

funannotate check message:

```console
$ funannotate check --show-versions
-------------------------------------------------------
Checking dependencies for 1.8.7
-------------------------------------------------------
You are running Python v 3.7.10. Now checking python packages...
biopython: 1.70
goatools: 1.1.6
matplotlib: 2.1.2
natsort: 7.0.1
numpy: 1.20.2
pandas: 0.24.1
psutil: 5.8.0
requests: 2.25.1
scikit-learn: 0.24.2
scipy: 1.4.1
seaborn: 0.11.1
All 11 python packages installed


You are running Perl v b'5.026002'. Now checking perl modules...
Bio::Perl: 1.007002
Carp: 1.38
Clone: 0.42
DBD::SQLite: 1.64
DBD::mysql: 4.046
DBI: 1.642
DB_File: 1.855
Data::Dumper: 2.173
File::Basename: 2.85
File::Which: 1.23
Getopt::Long: 2.5
Hash::Merge: 0.300
JSON: 4.02
LWP::UserAgent: 6.39
Logger::Simple: 2.0
POSIX: 1.76
Parallel::ForkManager: 2.02
Pod::Usage: 1.69
Scalar::Util::Numeric: 0.40
Storable: 3.15
Text::Soundex: 3.05
Thread::Queue: 3.12
Tie::File: 1.02
URI::Escape: 3.31
YAML: 1.29
threads: 2.15
threads::shared: 1.56
All 27 Perl modules installed


Checking Environmental Variables...
$FUNANNOTATE_DB=/nfs1/CGRB/databases/funannotate/current
$PASAHOME=/local/cluster/funannotate-1.8.7/opt/pasa-2.4.1
$TRINITY_HOME=/local/cluster/funannotate-1.8.7/opt/trinity-2.8.5
$EVM_HOME=/local/cluster/funannotate-1.8.7/opt/evidencemodeler-1.1.1
$AUGUSTUS_CONFIG_PATH=/local/cluster/funannotate-1.8.7/config/
$GENEMARK_PATH=/local/cluster/gmes_linux_64
All 6 environmental variables are set
-------------------------------------------------------
Checking external dependencies...
PASA: 2.4.1
CodingQuarry: 2.0
Trinity: 2.8.5
augustus: 3.3.3
bamtools: bamtools 2.5.1
bedtools: bedtools v2.30.0
blat: BLAT v36
diamond: 2.0.8
emapper.py: There was an error retrieving eggnog-mapper DB data: malformed database schema (prots) - near "WITHOUT": syntax error
Maybe you need to run download_eggnog_data.py
emapper-2.1.4-2 / Expected eggNOG DB version: 5.0.2 / Installed eggNOG DB version: unknown / Local diamond version: diamond 2.0.4 / Local MMseqs2 version: 113e3212c137d026e297c7540e1fcd039f6812b1

ete3: 3.1.2
exonerate: exonerate 2.4.0
fasta: no way to determine
glimmerhmm: 3.0.4
gmap: 2017-11-15
gmes_petap.pl: 4.62_lic
hisat2: 2.2.1
hmmscan: HMMER 3.3.2 (Nov 2020)
hmmsearch: HMMER 3.3.2 (Nov 2020)
java: 11.0.8-internal
kallisto: 0.46.1
mafft: v7.480 (2021/May/21)
makeblastdb: makeblastdb 2.2.31+
minimap2: 2.21-r1071
proteinortho: 6.0.31
pslCDnaFilter: no way to determine
salmon: salmon 0.14.1
samtools: samtools 1.10
signalp: 4.1
snap: 2006-07-28
stringtie: 2.1.7
tRNAscan-SE: 2.0.7 (Oct 2020)
tantan: tantan 26
tbl2asn: no way to determine, likely 25.X
tblastn: tblastn 2.2.31+
trimal: trimAl v1.4.rev15 build[2013-12-17]
trimmomatic: 0.39
All 36 external dependencies are installed
```

Funannotate can be used to annotate eukaryotic genomes. It was developed for
smaller genomes (e.g. less than 1GB in size).

software ref: <https://github.com/nextgenusfs/funannotate>  
software ref: <http://funannotate.readthedocs.io>  
research ref: <https://zenodo.org/record/4054262>