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:
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bash
source /local/cluster/funannotate/activate.sh
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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:
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(/local/cluster/funannotate-1.8.9) [cgrbinst@chrom1 funannotate]$ which funannotate
/local/cluster/funannotate-1.8.9/bin/funannotate
(/local/cluster/funannotate-1.8.9) [cgrbinst@chrom1 funannotate]$ funannotate --version
funannotate v1.8.9
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DB Path:
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$FUNANNOTATE_DB=/nfs1/CGRB/databases/funannotate/current
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help message:
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$ funannotate --help
Usage: funannotate <command> <arguments>
version: 1.8.9
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 --show-versions
-------------------------------------------------------
Checking dependencies for 1.8.9
-------------------------------------------------------
You are running Python v 3.8.11. Now checking python packages...
biopython: 1.77
goatools: 1.1.6
matplotlib: 3.4.3
natsort: 7.1.1
numpy: 1.21.2
pandas: 1.3.2
psutil: 5.8.0
requests: 2.26.0
scikit-learn: 0.24.2
scipy: 1.7.1
seaborn: 0.11.2
All 11 python packages installed
You are running Perl v b'5.026002'. Now checking perl modules...
Bio::Perl: 1.7.4
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-1.8.9/opt/pasa-2.4.1
$TRINITY_HOME=/local/cluster/funannotate-1.8.9/opt/trinity-2.8.5
$EVM_HOME=/local/cluster/funannotate-1.8.9/opt/evidencemodeler-1.1.1
$AUGUSTUS_CONFIG_PATH=/local/cluster/funannotate-1.8.9/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: 2.0.11
emapper.py: 2.1.5
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: 11.0.9.1-internal
kallisto: 0.46.1
mafft: v7.487 (2021/Jul/25)
makeblastdb: makeblastdb 2.2.31+
minimap2: 2.22-r1101
proteinortho: 6.0.31
pslCDnaFilter: no way to determine
salmon: salmon 0.14.1
samtools: samtools 1.12
signalp: 4.1
snap: 2006-07-28
stringtie: 2.1.7
tRNAscan-SE: 2.0.9 (July 2021)
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
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To use genemark (gmes_petap.pl) you need to run
bash /local/cluster/gmes_linux_64/setup.sh to get the license set up properly.
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