OrthoFinder-Sapelo2: Difference between revisions

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=== Version ===
=== Version ===
2.3.8, 2.3.11, 2.5.2
2.5.4


=== Author / Distributor ===
=== Author / Distributor ===
Line 21: Line 21:
=== Running Program ===
=== Running Program ===


Also refer to [[Running Jobs on Sapelo2]]
Please refer to [[Running Jobs on Sapelo2]]
Also refer to [[Running_Jobs_on_Sapelo2#Running_an_X-windows_application | Run X window Jobs]] and
[[Running_Jobs_on_Sapelo2#Running_an_Interactive_Job | Run interactive Jobs]]


*Version 2.3.8, installed at /apps/eb/OrthoFinder/2.3.8-foss-2019b-Python-2.7.16
*Version 2.5.4, installed at /apps/eb/OrthoFinder/2.5.4-foss-2022a/
*Version 2.3.11, installed at /apps/eb/OrthoFinder/2.3.11-intel-2019b-Python-3.7.4
*Version 2.5.2, installed at /apps/eb/OrthoFinder/2.5.2-foss-2019b-Python-3.7.4


To use the version 2.3.8, please first load the module with
To use the version 2.5.4, please first load the module with


<pre class="gscript">
<pre class="gscript">
ml OrthoFinder/2.3.8-foss-2019b-Python-2.7.16
ml OrthoFinder/2.5.4-foss-2022a
</pre>  
</pre>  


To use the version 2.3.1, please first load the module with


<pre class="gscript">
Here is an example of a shell script sub.sh to run orthofinder of version 2.5.4 at the batch queue:  
ml OrthoFinder/2.3.11-intel-2019b-Python-3.7.4
</pre>
 
To use the version 2.5.2, please first load the module with
 
<pre class="gscript">
ml OrthoFinder/2.5.2-foss-2019b-Python-3.7.4
</pre>
 
 
Here is an example of a shell script sub.sh to run orthofinder.py of version 2.5.2 at the batch queue:
<pre class="gscript">
#!/bin/bash
#PBS -N j_OrthoFinder
#PBS -q batch
#PBS -l nodes=1:ppn=1:AMD
#PBS -l walltime=480:00:00
#PBS -l mem=10gb
 
cd $PBS_O_WORKDIR
 
module load orthofinder/2.1.2
 
orthofinder.py [options] 1>job.out 2>job.err 
</pre>
 
Here is an example of a shell script sub.sh to run orthofinder.py of version 2.2.7 at the batch queue:  
<pre class="gscript">
<pre class="gscript">
#!/bin/bash
#!/bin/bash
#PBS -N j_OrthoFinder
#SBATCH --job-name=j_OrthoFinder  
#PBS -q batch
#SBATCH --partition=batch          
#PBS -l nodes=1:ppn=1
#SBATCH --ntasks=1                
#PBS -l walltime=480:00:00
#SBATCH --cpus-per-task=8     
#PBS -l mem=10gb
#SBATCH --mem=32gb                   
#SBATCH --time=120:00:00          
#SBATCH --output=log.%j.out   
#SBATCH --error=log.%j.err         
#SBATCH --mail-user=username@uga.edu 
#SBATCH --mail-type=ALL 


cd $PBS_O_WORKDIR
cd $SLURM_SUBMIT_DIR


module load OrthoFinder/2.2.7-foss-2018a-Python-2.7.14
ml OrthoFinder/2.5.4-foss-2022a


orthofinder.py [options] 1>job.out 2>job.err    
orthofinder -t 8 -a 8 [options]   
</pre>
</pre>


Here is an example of a shell script sub.sh to run orthofinder.py of version 2.3.7 at the batch queue:
<pre class="gscript">
#!/bin/bash
#PBS -N j_OrthoFinder
#PBS -q batch
#PBS -l nodes=1:ppn=1
#PBS -l walltime=480:00:00
#PBS -l mem=10gb
cd $PBS_O_WORKDIR
module load OrthoFinder/2.3.7-foss-2018a-Python-2.7.14
module load BLAST+/2.7.1-foss-2018a
module load MAFFT/7.407-foss-2018a-with-extensions
orthofinder.py [options] 1>job.out 2>job.err
</pre>


Here is an example of job submission
Here is an example of job submission
<pre  class="gcommand">
<pre  class="gcommand">
qsub  ./sub.sh  
sbatch ./sub.sh  
</pre>
</pre>


=== Documentation ===
=== Documentation ===
   
   
<pre class="gcommand">
<pre class="gcommand">
ml OrthoFinder/2.5.4-foss-2022a
orthofinder -h


module load orthofinder/2.1.2
OrthoFinder version 2.5.4 Copyright (C) 2014 David Emms
orthofinder.py -h
 
OrthoFinder version 2.1.2 Copyright (C) 2014 David Emms


SIMPLE USAGE:
SIMPLE USAGE:
Line 120: Line 75:


OPTIONS:
OPTIONS:
  -t <int>         Number of parallel sequence search threads [Default = 16]
  -t <int>       Number of parallel sequence search threads [Default = 16]
  -a <int>         Number of parallel analysis threads [Default = 1]
  -a <int>       Number of parallel analysis threads
  -M <txt>         Method for gene tree inference. Options 'dendroblast' & 'msa'
-d              Input is DNA sequences
                  [Default = dendroblast]
  -M <txt>       Method for gene tree inference. Options 'dendroblast' & 'msa'
  -S <txt>         Sequence search program [Default = blast]
                [Default = dendroblast]
                  Options: blast, blast_gz, diamond
  -S <txt>       Sequence search program [Default = diamond]
  -A <txt>         MSA program, requires '-M msa' [Default = mafft]
                Options: blast, diamond, diamond_ultra_sens, blast_gz, mmseqs, blast_nucl
                  Options: mafft, muscle, mafft
  -A <txt>       MSA program, requires '-M msa' [Default = mafft]
  -T <txt>         Tree inference method, requires '-M msa' [Default = fasttree]
                Options: mafft, muscle
                  Options: mafft, iqtree, fasttree, raxml
  -T <txt>       Tree inference method, requires '-M msa' [Default = fasttree]
-R <txt>          Tree reconciliation method [Default = of_recon]
                Options: fasttree, raxml, raxml-ng, iqtree
                  Options: of_recon, dlcpar, dlcpar_deepsearch
  -s <file>       User-specified rooted species tree
  -s <file>         User-specified rooted species tree
  -I <int>       MCL inflation parameter [Default = 1.5]
  -I <int>         MCL inflation parameter [Default = 1.5]
  -x <file>       Info for outputting results in OrthoXML format
  -x <file>         Info for outputting results in OrthoXML format
  -p <dir>       Write the temporary pickle files to <dir>
  -p <dir>         Write the temporary pickle files to <dir>
  -1             Only perform one-way sequence search
  -1               Only perform one-way sequence search  
-X              Don't add species names to sequence IDs
  -n <txt>         Name to append to the results directory
-y              Split paralogous clades below root of a HOG into separate HOGs
  -h               Print this help text
-z              Don't trim MSAs (columns>=90% gap, min. alignment length 500)
  -n <txt>       Name to append to the results directory
-o <txt>        Non-default results directory
  -h             Print this help text


WORKFLOW STOPPING OPTIONS:
WORKFLOW STOPPING OPTIONS:
  -op               Stop after preparing input files for BLAST
  -op             Stop after preparing input files for BLAST
  -og               Stop after inferring orthogroups
  -og             Stop after inferring orthogroups
  -os               Stop after writing sequence files for orthogroups
  -os             Stop after writing sequence files for orthogroups
                  (requires '-M msa')
                (requires '-M msa')
  -oa               Stop after inferring alignments for orthogroups
  -oa             Stop after inferring alignments for orthogroups
                  (requires '-M msa')
                (requires '-M msa')
  -ot               Stop after inferring gene trees for orthogroups  
  -ot             Stop after inferring gene trees for orthogroups  


WORKFLOW RESTART COMMANDS:
WORKFLOW RESTART COMMANDS:
Line 159: Line 117:
CITATION:
CITATION:
  When publishing work that uses OrthoFinder please cite:
  When publishing work that uses OrthoFinder please cite:
  Emms D.M. & Kelly S. (2015), Genome Biology 16:157
  Emms D.M. & Kelly S. (2019), Genome Biology 20:238
 
If you use the species tree in your work then please also cite:
Emms D.M. & Kelly S. (2017), MBE 34(12): 3267-3278
Emms D.M. & Kelly S. (2018), bioRxiv https://doi.org/10.1101/267914
</pre>
</pre>
[[#top|Back to Top]]
[[#top|Back to Top]]

Revision as of 11:46, 5 September 2023

Category

Bioinformatics

Program On

Sapelo2

Version

2.5.4

Author / Distributor

OrthoFinder

Description

"OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics. It finds orthologues and orthogroups infers rooted gene trees for all orthogroups and infers a rooted species tree for the species being analysed. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. OrthoFinder is simple to use and all you need to run it is a set of protein sequence files (one per species) in FASTA format." More details are at OrthoFinder

Running Program

Please refer to Running Jobs on Sapelo2

  • Version 2.5.4, installed at /apps/eb/OrthoFinder/2.5.4-foss-2022a/

To use the version 2.5.4, please first load the module with 

ml OrthoFinder/2.5.4-foss-2022a


Here is an example of a shell script sub.sh to run orthofinder of version 2.5.4 at the batch queue: 

#!/bin/bash
#SBATCH --job-name=j_OrthoFinder   
#SBATCH --partition=batch            
#SBATCH --ntasks=1                  	
#SBATCH --cpus-per-task=8       
#SBATCH --mem=32gb                    
#SBATCH --time=120:00:00           
#SBATCH --output=log.%j.out     
#SBATCH --error=log.%j.err          
#SBATCH --mail-user=username@uga.edu  
#SBATCH --mail-type=ALL   

cd $SLURM_SUBMIT_DIR

ml OrthoFinder/2.5.4-foss-2022a

orthofinder -t 8 -a 8 [options]


Here is an example of job submission 

sbatch ./sub.sh

Documentation

ml OrthoFinder/2.5.4-foss-2022a 
orthofinder -h

OrthoFinder version 2.5.4 Copyright (C) 2014 David Emms

SIMPLE USAGE:
Run full OrthoFinder analysis on FASTA format proteomes in <dir>
  orthofinder [options] -f <dir>

Add new species in <dir1> to previous run in <dir2> and run new analysis
  orthofinder [options] -f <dir1> -b <dir2>

OPTIONS:
 -t <int>        Number of parallel sequence search threads [Default = 16]
 -a <int>        Number of parallel analysis threads
 -d              Input is DNA sequences
 -M <txt>        Method for gene tree inference. Options 'dendroblast' & 'msa'
                 [Default = dendroblast]
 -S <txt>        Sequence search program [Default = diamond]
                 Options: blast, diamond, diamond_ultra_sens, blast_gz, mmseqs, blast_nucl
 -A <txt>        MSA program, requires '-M msa' [Default = mafft]
                 Options: mafft, muscle
 -T <txt>        Tree inference method, requires '-M msa' [Default = fasttree]
                 Options: fasttree, raxml, raxml-ng, iqtree
 -s <file>       User-specified rooted species tree
 -I <int>        MCL inflation parameter [Default = 1.5]
 -x <file>       Info for outputting results in OrthoXML format
 -p <dir>        Write the temporary pickle files to <dir>
 -1              Only perform one-way sequence search
 -X              Don't add species names to sequence IDs
 -y              Split paralogous clades below root of a HOG into separate HOGs
 -z              Don't trim MSAs (columns>=90% gap, min. alignment length 500)
 -n <txt>        Name to append to the results directory
 -o <txt>        Non-default results directory
 -h              Print this help text

WORKFLOW STOPPING OPTIONS:
 -op             Stop after preparing input files for BLAST
 -og             Stop after inferring orthogroups
 -os             Stop after writing sequence files for orthogroups
                 (requires '-M msa')
 -oa             Stop after inferring alignments for orthogroups
                 (requires '-M msa')
 -ot             Stop after inferring gene trees for orthogroups 

WORKFLOW RESTART COMMANDS:
 -b  <dir>         Start OrthoFinder from pre-computed BLAST results in <dir>
 -fg <dir>         Start OrthoFinder from pre-computed orthogroups in <dir>
 -ft <dir>         Start OrthoFinder from pre-computed gene trees in <dir>

LICENSE:
 Distributed under the GNU General Public License (GPLv3). See License.md

CITATION:
 When publishing work that uses OrthoFinder please cite:
 Emms D.M. & Kelly S. (2019), Genome Biology 20:238

 If you use the species tree in your work then please also cite:
 Emms D.M. & Kelly S. (2017), MBE 34(12): 3267-3278
 Emms D.M. & Kelly S. (2018), bioRxiv https://doi.org/10.1101/267914

Back to Top

Installation

source code from OrthoFinder

System

64-bit Linux

Retrieved from "https://wiki.gacrc.uga.edu/index.php?title=OrthoFinder-Sapelo2&oldid=21300"