OrthoFinder
Introduction
OrthoFinder [1] is an orthology detector seen in some circles as better than the widely used OrthoMCL.
Usage patterns
Many taken from OrthoFinder's githib page linked below.
Can be verbose as outputs are included.
First we make sure to get the right
$ module unload python/2.7
$ module load python/2.7.11 OrthoFinder
Currently Loaded Modulefiles:
1) modules 2) python/2.7 3) R/3.2.1 4) blastall/2.2.26 5) blastScripts/1.0.0 6) openmpi/1.6.5 7) mcl/14-137 8) mafft/7.147 9) FastTree/2.1.8 10) OrthoFinder/0.6.0
$ orthofinder.py -f ExampleDataset/
OrthoFinder version 0.6.0 Copyright (C) 2014 David Emms
This program comes with ABSOLUTELY NO WARRANTY.
This is free software, and you are welcome to redistribute it under certain conditions.
For details please see the License.md that came with this software.
1 threads for OrthoFinder algorithm
1. Checking required programs are installed
-------------------------------------------
Test can run "makeblastdb -help" - ok
Test can run "blastp -help" - ok
Test can run "mcl -h" - ok
2. Temporarily renaming sequences with unique, simple identifiers
------------------------------------------------------------------
Done
3. Dividing up work for BLAST for parallel processing
-----------------------------------------------------
3a. Creating BLAST databases
----------------------------
Building a new DB, current time: 06/21/2016 21:52:11
New DB name: /shelf/scratch/ramon/swmake/OrthoFinder-0.6/ExampleDataset/Results_Jun21/WorkingDirectory/BlastDBSpecies0
New DB title: /shelf/scratch/ramon/swmake/OrthoFinder-0.6/ExampleDataset/Results_Jun21/WorkingDirectory/Species0.fa
Sequence type: Protein
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 820 sequences in 0.0515079 seconds.
Building a new DB, current time: 06/21/2016 21:52:11
New DB name: /shelf/scratch/ramon/swmake/OrthoFinder-0.6/ExampleDataset/Results_Jun21/WorkingDirectory/BlastDBSpecies1
New DB title: /shelf/scratch/ramon/swmake/OrthoFinder-0.6/ExampleDataset/Results_Jun21/WorkingDirectory/Species1.fa
Sequence type: Protein
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 763 sequences in 0.0477939 seconds.
Building a new DB, current time: 06/21/2016 21:52:11
New DB name: /shelf/scratch/ramon/swmake/OrthoFinder-0.6/ExampleDataset/Results_Jun21/WorkingDirectory/BlastDBSpecies2
New DB title: /shelf/scratch/ramon/swmake/OrthoFinder-0.6/ExampleDataset/Results_Jun21/WorkingDirectory/Species2.fa
Sequence type: Protein
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 476 sequences in 0.03089 seconds.
Building a new DB, current time: 06/21/2016 21:52:11
New DB name: /shelf/scratch/ramon/swmake/OrthoFinder-0.6/ExampleDataset/Results_Jun21/WorkingDirectory/BlastDBSpecies3
New DB title: /shelf/scratch/ramon/swmake/OrthoFinder-0.6/ExampleDataset/Results_Jun21/WorkingDirectory/Species3.fa
Sequence type: Protein
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 674 sequences in 0.0401189 seconds.
4. Running BLAST all-versus-all
-------------------------------
Maximum number of BLAST processes: 16
2016-06-21 21:52:11 : This may take some time....
2016-06-21 21:52:11 : Running Blast 0 of 16
2016-06-21 21:52:11 : Running Blast 1 of 16
2016-06-21 21:52:11 : Running Blast 2 of 16
2016-06-21 21:52:11 : Running Blast 3 of 16
2016-06-21 21:52:11 : Running Blast 4 of 16
2016-06-21 21:52:11 : Running Blast 6 of 16
2016-06-21 21:52:11 : Running Blast 5 of 16
2016-06-21 21:52:11 : Running Blast 7 of 16
2016-06-21 21:52:11 : Running Blast 8 of 16
2016-06-21 21:52:11 : Running Blast 9 of 16
2016-06-21 21:52:11 : Running Blast 11 of 16
2016-06-21 21:52:11 : Running Blast 10 of 16
2016-06-21 21:52:11 : Running Blast 12 of 16
2016-06-21 21:52:11 : Running Blast 13 of 16
2016-06-21 21:52:11 : Running Blast 14 of 16
2016-06-21 21:52:11 : Running Blast 15 of 16
2016-06-21 21:52:17 : Finished Blast 15 of 16
2016-06-21 21:52:18 : Finished Blast 9 of 16
2016-06-21 21:52:19 : Finished Blast 14 of 16
2016-06-21 21:52:19 : Finished Blast 13 of 16
2016-06-21 21:52:19 : Finished Blast 10 of 16
2016-06-21 21:52:20 : Finished Blast 11 of 16
2016-06-21 21:52:20 : Finished Blast 12 of 16
2016-06-21 21:52:23 : Finished Blast 6 of 16
2016-06-21 21:52:23 : Finished Blast 7 of 16
2016-06-21 21:52:23 : Finished Blast 2 of 16
2016-06-21 21:52:23 : Finished Blast 4 of 16
2016-06-21 21:52:23 : Finished Blast 5 of 16
2016-06-21 21:52:24 : Finished Blast 1 of 16
2016-06-21 21:52:25 : Finished Blast 8 of 16
2016-06-21 21:52:28 : Finished Blast 0 of 16
2016-06-21 21:52:30 : Finished Blast 3 of 16
Done!
5. Running OrthoFinder algorithm
--------------------------------
2016-06-21 21:52:31 : Initial processing of each species
2016-06-21 21:52:31 : Starting species 0
2016-06-21 21:52:31 : Initial processing of species 0 complete
2016-06-21 21:52:31 : Starting species 1
2016-06-21 21:52:32 : Initial processing of species 1 complete
2016-06-21 21:52:32 : Starting species 2
2016-06-21 21:52:32 : Initial processing of species 2 complete
2016-06-21 21:52:32 : Starting species 3
2016-06-21 21:52:32 : Initial processing of species 3 complete
2016-06-21 21:52:34 : Connected putatitive homologs
2016-06-21 21:52:35 : Writen final scores for species 2 to graph file
2016-06-21 21:52:35 : Writen final scores for species 3 to graph file
2016-06-21 21:52:35 : Writen final scores for species 1 to graph file
2016-06-21 21:52:35 : Writen final scores for species 0 to graph file
[mclIO] reading </shelf/scratch/ramon/swmake/OrthoFinder-0.6/ExampleDataset/Results_Jun21/WorkingDirectory/OrthoFinder_v0.6.0_graph.txt>
.......................................
[mclIO] read native interchange 2733x2733 matrix with 5080 entries
[mcl] pid 23551
ite chaos time hom(avg,lo,hi) m-ie m-ex i-ex fmv
1 19.76 0.00 0.99/0.04/1.42 1.67 1.67 1.67 0
2 15.38 0.00 0.94/0.39/1.23 1.47 1.20 2.01 4
3 7.67 0.01 0.93/0.42/1.12 1.25 0.91 1.83 5
4 6.63 0.01 0.92/0.39/1.22 1.22 0.73 1.33 5
5 5.23 0.00 0.91/0.25/1.20 1.20 0.90 1.19 2
6 4.25 0.02 0.89/0.38/1.20 1.17 0.92 1.10 1
7 3.53 0.01 0.88/0.46/1.00 1.08 0.93 1.02 0
8 2.30 0.01 0.88/0.50/1.00 1.05 0.94 0.95 0
9 1.13 0.01 0.88/0.55/1.00 1.02 0.94 0.89 0
10 1.04 0.01 0.90/0.55/1.00 1.02 0.94 0.84 0
11 0.73 0.00 0.92/0.50/1.00 1.00 0.93 0.78 0
12 0.64 0.01 0.94/0.63/1.00 1.00 0.91 0.71 0
13 0.66 0.00 0.96/0.62/1.00 1.00 0.91 0.64 0
14 0.67 0.00 0.97/0.62/1.00 1.00 0.88 0.57 0
15 0.52 0.00 0.98/0.69/1.00 1.00 0.91 0.52 0
16 0.50 0.01 0.99/0.75/1.00 1.00 0.91 0.47 0
17 0.42 0.01 0.99/0.59/1.00 1.00 0.95 0.45 0
18 0.25 0.01 0.99/0.57/1.00 1.00 0.96 0.43 0
19 0.25 0.00 1.00/0.77/1.00 1.00 0.99 0.42 0
20 0.25 0.01 1.00/0.77/1.00 1.00 0.98 0.42 0
21 0.24 0.00 1.00/0.77/1.00 1.00 0.98 0.41 0
22 0.24 0.01 1.00/0.76/1.00 1.00 0.99 0.41 0
23 0.18 0.00 1.00/0.83/1.00 1.00 0.99 0.40 0
24 0.24 0.00 1.00/0.89/1.00 1.00 1.00 0.40 0
25 0.33 0.01 1.00/0.80/1.00 1.00 1.00 0.40 0
26 0.44 0.00 1.00/0.68/1.00 1.00 1.00 0.40 0
27 0.50 0.00 1.00/0.63/1.00 1.00 1.00 0.40 0
28 0.44 0.00 1.00/0.69/1.00 1.00 1.00 0.40 0
29 0.24 0.00 1.00/0.84/1.00 1.00 1.00 0.40 0
30 0.06 0.00 1.00/0.96/1.00 1.00 1.00 0.40 0
31 0.01 0.01 1.00/1.00/1.00 1.00 1.00 0.40 0
32 0.00 0.00 1.00/1.00/1.00 1.00 0.99 0.40 0
[mcl] jury pruning marks: <100,99,99>, out of 100
[mcl] jury pruning synopsis: <99.6 or perfect> (cf -scheme, -do log)
[mclIO] writing </shelf/scratch/ramon/swmake/OrthoFinder-0.6/ExampleDataset/Results_Jun21/WorkingDirectory/clusters_OrthoFinder_v0.6.0_I1.5.txt>
.......................................
[mclIO] wrote native interchange 2733x1331 matrix with 2733 entries to stream </shelf/scratch/ramon/swmake/OrthoFinder-0.6/ExampleDataset/Results_Jun21/WorkingDirectory/clusters_OrthoFinder_v0.6.0_I1.5.txt>
[mcl] 1331 clusters found
[mcl] output is in /shelf/scratch/ramon/swmake/OrthoFinder-0.6/ExampleDataset/Results_Jun21/WorkingDirectory/clusters_OrthoFinder_v0.6.0_I1.5.txt
Please cite:
Stijn van Dongen, Graph Clustering by Flow Simulation. PhD thesis,
University of Utrecht, May 2000.
( http://www.library.uu.nl/digiarchief/dip/diss/1895620/full.pdf
or http://micans.org/mcl/lit/svdthesis.pdf.gz)
OR
Stijn van Dongen, A cluster algorithm for graphs. Technical
Report INS-R0010, National Research Institute for Mathematics
and Computer Science in the Netherlands, Amsterdam, May 2000.
( http://www.cwi.nl/ftp/CWIreports/INS/INS-R0010.ps.Z
or http://micans.org/mcl/lit/INS-R0010.ps.Z)
2016-06-21 21:52:35 : Ran MCL
6. Creating files for Orthologous Groups
--------------------------------------- $ module unload python/2.7
$ module load python/2.7.11 OrthoFinder
Currently Loaded Modulefiles:
1) modules 2) python/2.7 3) R/3.2.1 4) blastall/2.2.26 5) blastScripts/1.0.0 6) openmpi/1.6.5 7) mcl/14-137 8) mafft/7.147 9) FastTree/2.1.8 10) OrthoFinder/0.6.0
$ orthofinder.py -f ExampleDataset/
OrthoFinder version 0.6.0 Copyright (C) 2014 David Emms
This program comes with ABSOLUTELY NO WARRANTY.
This is free software, and you are welcome to redistribute it under certain conditions.
For details please see the License.md that came with this software.
1 threads for OrthoFinder algorithm
1. Checking required programs are installed
-------------------------------------------
Test can run "makeblastdb -help" - ok
Test can run "blastp -help" - ok
Test can run "mcl -h" - ok
2. Temporarily renaming sequences with unique, simple identifiers
------------------------------------------------------------------
Done
3. Dividing up work for BLAST for parallel processing
-----------------------------------------------------
3a. Creating BLAST databases
----------------------------
Building a new DB, current time: 06/21/2016 21:52:11
New DB name: /shelf/scratch/ramon/swmake/OrthoFinder-0.6/ExampleDataset/Results_Jun21/WorkingDirectory/BlastDBSpecies0
New DB title: /shelf/scratch/ramon/swmake/OrthoFinder-0.6/ExampleDataset/Results_Jun21/WorkingDirectory/Species0.fa
Sequence type: Protein
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 820 sequences in 0.0515079 seconds.
Building a new DB, current time: 06/21/2016 21:52:11
New DB name: /shelf/scratch/ramon/swmake/OrthoFinder-0.6/ExampleDataset/Results_Jun21/WorkingDirectory/BlastDBSpecies1
New DB title: /shelf/scratch/ramon/swmake/OrthoFinder-0.6/ExampleDataset/Results_Jun21/WorkingDirectory/Species1.fa
Sequence type: Protein
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 763 sequences in 0.0477939 seconds.
Building a new DB, current time: 06/21/2016 21:52:11
New DB name: /shelf/scratch/ramon/swmake/OrthoFinder-0.6/ExampleDataset/Results_Jun21/WorkingDirectory/BlastDBSpecies2
New DB title: /shelf/scratch/ramon/swmake/OrthoFinder-0.6/ExampleDataset/Results_Jun21/WorkingDirectory/Species2.fa
Sequence type: Protein
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 476 sequences in 0.03089 seconds.
Building a new DB, current time: 06/21/2016 21:52:11
New DB name: /shelf/scratch/ramon/swmake/OrthoFinder-0.6/ExampleDataset/Results_Jun21/WorkingDirectory/BlastDBSpecies3
New DB title: /shelf/scratch/ramon/swmake/OrthoFinder-0.6/ExampleDataset/Results_Jun21/WorkingDirectory/Species3.fa
Sequence type: Protein
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 674 sequences in 0.0401189 seconds.
4. Running BLAST all-versus-all
-------------------------------
Maximum number of BLAST processes: 16
2016-06-21 21:52:11 : This may take some time....
2016-06-21 21:52:11 : Running Blast 0 of 16
2016-06-21 21:52:11 : Running Blast 1 of 16
2016-06-21 21:52:11 : Running Blast 2 of 16
2016-06-21 21:52:11 : Running Blast 3 of 16
2016-06-21 21:52:11 : Running Blast 4 of 16
2016-06-21 21:52:11 : Running Blast 6 of 16
2016-06-21 21:52:11 : Running Blast 5 of 16
2016-06-21 21:52:11 : Running Blast 7 of 16
2016-06-21 21:52:11 : Running Blast 8 of 16
2016-06-21 21:52:11 : Running Blast 9 of 16
2016-06-21 21:52:11 : Running Blast 11 of 16
2016-06-21 21:52:11 : Running Blast 10 of 16
2016-06-21 21:52:11 : Running Blast 12 of 16
2016-06-21 21:52:11 : Running Blast 13 of 16
2016-06-21 21:52:11 : Running Blast 14 of 16
2016-06-21 21:52:11 : Running Blast 15 of 16
2016-06-21 21:52:17 : Finished Blast 15 of 16
2016-06-21 21:52:18 : Finished Blast 9 of 16
2016-06-21 21:52:19 : Finished Blast 14 of 16
2016-06-21 21:52:19 : Finished Blast 13 of 16
2016-06-21 21:52:19 : Finished Blast 10 of 16
2016-06-21 21:52:20 : Finished Blast 11 of 16
2016-06-21 21:52:20 : Finished Blast 12 of 16
2016-06-21 21:52:23 : Finished Blast 6 of 16
2016-06-21 21:52:23 : Finished Blast 7 of 16
2016-06-21 21:52:23 : Finished Blast 2 of 16
2016-06-21 21:52:23 : Finished Blast 4 of 16
2016-06-21 21:52:23 : Finished Blast 5 of 16
2016-06-21 21:52:24 : Finished Blast 1 of 16
2016-06-21 21:52:25 : Finished Blast 8 of 16
2016-06-21 21:52:28 : Finished Blast 0 of 16
2016-06-21 21:52:30 : Finished Blast 3 of 16
Done!
5. Running OrthoFinder algorithm
--------------------------------
2016-06-21 21:52:31 : Initial processing of each species
2016-06-21 21:52:31 : Starting species 0
2016-06-21 21:52:31 : Initial processing of species 0 complete
2016-06-21 21:52:31 : Starting species 1
2016-06-21 21:52:32 : Initial processing of species 1 complete
2016-06-21 21:52:32 : Starting species 2
2016-06-21 21:52:32 : Initial processing of species 2 complete
2016-06-21 21:52:32 : Starting species 3
2016-06-21 21:52:32 : Initial processing of species 3 complete
2016-06-21 21:52:34 : Connected putatitive homologs
2016-06-21 21:52:35 : Writen final scores for species 2 to graph file
2016-06-21 21:52:35 : Writen final scores for species 3 to graph file
2016-06-21 21:52:35 : Writen final scores for species 1 to graph file
2016-06-21 21:52:35 : Writen final scores for species 0 to graph file
[mclIO] reading </shelf/scratch/ramon/swmake/OrthoFinder-0.6/ExampleDataset/Results_Jun21/WorkingDirectory/OrthoFinder_v0.6.0_graph.txt>
.......................................
[mclIO] read native interchange 2733x2733 matrix with 5080 entries
[mcl] pid 23551
ite chaos time hom(avg,lo,hi) m-ie m-ex i-ex fmv
1 19.76 0.00 0.99/0.04/1.42 1.67 1.67 1.67 0
2 15.38 0.00 0.94/0.39/1.23 1.47 1.20 2.01 4
3 7.67 0.01 0.93/0.42/1.12 1.25 0.91 1.83 5
4 6.63 0.01 0.92/0.39/1.22 1.22 0.73 1.33 5
5 5.23 0.00 0.91/0.25/1.20 1.20 0.90 1.19 2
6 4.25 0.02 0.89/0.38/1.20 1.17 0.92 1.10 1
7 3.53 0.01 0.88/0.46/1.00 1.08 0.93 1.02 0
8 2.30 0.01 0.88/0.50/1.00 1.05 0.94 0.95 0
9 1.13 0.01 0.88/0.55/1.00 1.02 0.94 0.89 0
10 1.04 0.01 0.90/0.55/1.00 1.02 0.94 0.84 0
11 0.73 0.00 0.92/0.50/1.00 1.00 0.93 0.78 0
12 0.64 0.01 0.94/0.63/1.00 1.00 0.91 0.71 0
13 0.66 0.00 0.96/0.62/1.00 1.00 0.91 0.64 0
14 0.67 0.00 0.97/0.62/1.00 1.00 0.88 0.57 0
15 0.52 0.00 0.98/0.69/1.00 1.00 0.91 0.52 0
16 0.50 0.01 0.99/0.75/1.00 1.00 0.91 0.47 0
17 0.42 0.01 0.99/0.59/1.00 1.00 0.95 0.45 0
18 0.25 0.01 0.99/0.57/1.00 1.00 0.96 0.43 0
19 0.25 0.00 1.00/0.77/1.00 1.00 0.99 0.42 0
20 0.25 0.01 1.00/0.77/1.00 1.00 0.98 0.42 0
21 0.24 0.00 1.00/0.77/1.00 1.00 0.98 0.41 0
22 0.24 0.01 1.00/0.76/1.00 1.00 0.99 0.41 0
23 0.18 0.00 1.00/0.83/1.00 1.00 0.99 0.40 0
24 0.24 0.00 1.00/0.89/1.00 1.00 1.00 0.40 0
25 0.33 0.01 1.00/0.80/1.00 1.00 1.00 0.40 0
26 0.44 0.00 1.00/0.68/1.00 1.00 1.00 0.40 0
27 0.50 0.00 1.00/0.63/1.00 1.00 1.00 0.40 0
28 0.44 0.00 1.00/0.69/1.00 1.00 1.00 0.40 0
29 0.24 0.00 1.00/0.84/1.00 1.00 1.00 0.40 0
30 0.06 0.00 1.00/0.96/1.00 1.00 1.00 0.40 0
31 0.01 0.01 1.00/1.00/1.00 1.00 1.00 0.40 0
32 0.00 0.00 1.00/1.00/1.00 1.00 0.99 0.40 0
[mcl] jury pruning marks: <100,99,99>, out of 100
[mcl] jury pruning synopsis: <99.6 or perfect> (cf -scheme, -do log)
[mclIO] writing </shelf/scratch/ramon/swmake/OrthoFinder-0.6/ExampleDataset/Results_Jun21/WorkingDirectory/clusters_OrthoFinder_v0.6.0_I1.5.txt>
.......................................
[mclIO] wrote native interchange 2733x1331 matrix with 2733 entries to stream </shelf/scratch/ramon/swmake/OrthoFinder-0.6/ExampleDataset/Results_Jun21/WorkingDirectory/clusters_OrthoFinder_v0.6.0_I1.5.txt>
[mcl] 1331 clusters found
[mcl] output is in /shelf/scratch/ramon/swmake/OrthoFinder-0.6/ExampleDataset/Results_Jun21/WorkingDirectory/clusters_OrthoFinder_v0.6.0_I1.5.txt
Please cite:
Stijn van Dongen, Graph Clustering by Flow Simulation. PhD thesis,
University of Utrecht, May 2000.
( http://www.library.uu.nl/digiarchief/dip/diss/1895620/full.pdf
or http://micans.org/mcl/lit/svdthesis.pdf.gz)
OR
Stijn van Dongen, A cluster algorithm for graphs. Technical
Report INS-R0010, National Research Institute for Mathematics
and Computer Science in the Netherlands, Amsterdam, May 2000.
( http://www.cwi.nl/ftp/CWIreports/INS/INS-R0010.ps.Z
or http://micans.org/mcl/lit/INS-R0010.ps.Z)
2016-06-21 21:52:35 : Ran MCL
6. Creating files for Orthologous Groups
----------------------------------------
When publishing work that uses OrthoFinder please cite:
D.M. Emms & S. Kelly (2015), OrthoFinder: solving fundamental biases in whole genome comparisons
dramatically improves orthogroup inference accuracy, Genome Biology 16:157.
Orthologous groups have been written to tab-delimited files:
/shelf/scratch/ramon/swmake/OrthoFinder-0.6/ExampleDataset/Results_Jun21/OrthologousGroups.csv
/shelf/scratch/ramon/swmake/OrthoFinder-0.6/ExampleDataset/Results_Jun21/OrthologousGroups_UnassignedGenes.csv
And in OrthoMCL format:
/shelf/scratch/ramon/swmake/OrthoFinder-0.6/ExampleDataset/Results_Jun21/OrthologousGroups.txt
When publishing work that uses OrthoFinder please cite:
D.M. Emms & S. Kelly (2015), OrthoFinder: solving fundamental biases in whole genome comparisons
dramatically improves orthogroup inference accuracy, Genome Biology 16:157.
Orthologous groups have been written to tab-delimited files:
/shelf/scratch/ramon/swmake/OrthoFinder-0.6/ExampleDataset/Results_Jun21/OrthologousGroups.csv
/shelf/scratch/ramon/swmake/OrthoFinder-0.6/ExampleDataset/Results_Jun21/OrthologousGroups_UnassignedGenes.csv
And in OrthoMCL format:
/shelf/scratch/ramon/swmake/OrthoFinder-0.6/ExampleDataset/Results_Jun21/OrthologousGroups.txt
Links
- OrthoFinder's github page with some usage details
References
- ↑ D.M. Emms & S. Kelly (2015), OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy, Genome Biology 16:157.
