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davidemms / OrthoFinder

Phylogenetic orthology inference for comparative genomics
https://davidemms.github.io/
GNU General Public License v3.0
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path troubles #318

Closed desmondramirez closed 4 years ago

desmondramirez commented 4 years ago

Hi David,

When I try to run orthofinder, I get an error that it can't run diamond makeblastdb or blastp and to check my path. However, when I check my path using which, diamond pops up, and I am able to call it from command line. This happens even when I install orthofinder using conda (I have tried using both the source code and Bioconda installs).

Any ideas?

Thanks, Des

ddiazescandon commented 4 years ago

Hey, this is a different David. I had the same issue, and the only way I managed to "solve it" was using an older version in python 2.7 environment. (It's not solve at all)

OrthoFinder version 2.3.8 Copyright (C) 2014 David Emms

2019-12-12 18:13:45 : Starting OrthoFinder
8 thread(s) for highly parallel tasks (BLAST searches etc.)
8 thread(s) for OrthoFinder algorithm

Checking required programs are installed
----------------------------------------
ERROR: Cannot run diamond
Format of make database command:
  diamond makedb --in INPUT -d OUTPUT
ERROR: Cannot run diamond
Format of search database command:
  diamond blastp -d DATABASE -q INPUT -o OUTPUT -p 1 --quiet -e 0.001 --compress 1
Please check diamond is installed and that the executables are in the system path

If I try the same in a python 2.7. environment 

OrthoFinder version 2.3.8 Copyright (C) 2014 David Emms

2019-12-12 17:57:50 : Starting OrthoFinder
8 thread(s) for highly parallel tasks (BLAST searches etc.)
8 thread(s) for OrthoFinder algorithm

Checking required programs are installed
----------------------------------------
Test can run "makeblastdb -help" - ok
Test can run "blastp -help" - ok
Test can run "mcl -h" - failed

stdout:

stderr:
/bin/sh: /Users/daviddiaz/opt/anaconda3/envs/py2/bin/scripts_of/bin/mcl: cannot execute binary file

ERROR: Cannot run MCL with the command "mcl -h"
Please check MCL is installed and in the system path

And if I use an older version (using blast)

It run smoothly 

OrthoFinder version 2.2.7 Copyright (C) 2014 David Emms

2019-12-12 18:09:12 : Starting OrthoFinder
8 thread(s) for highly parallel tasks (BLAST searches etc.)
8 thread(s) for OrthoFinder algorithm

Checking required programs are installed
----------------------------------------
Test can run "makeblastdb -help" - ok
Test can run "blastp -help" - ok
Test can run "mcl -h" - ok
Test can run "fastme -i /Users/daviddiaz/Downloads/test/SimpleTest.phy -o /Users/daviddiaz/Downloads/test/SimpleTest.tre" - ok

Dividing up work for BLAST for parallel processing
--------------------------------------------------
2019-12-12 18:09:12 : Creating Blast database 1 of 4
2019-12-12 18:09:12 : Creating Blast database 2 of 4
2019-12-12 18:09:12 : Creating Blast database 3 of 4
2019-12-12 18:09:12 : Creating Blast database 4 of 4

Running BLAST all-versus-all
----------------------------
Using 8 thread(s)
2019-12-12 18:09:12 : This may take some time....
2019-12-12 18:09:12 : Done 0 of 16
2019-12-12 18:09:35 : Done all-versus-all sequence search

Running OrthoFinder algorithm
-----------------------------
2019-12-12 18:09:35 : Initial processing of each species
2019-12-12 18:09:36 : Initial processing of species 2 complete
2019-12-12 18:09:36 : Initial processing of species 3 complete
2019-12-12 18:09:36 : Initial processing of species 0 complete
2019-12-12 18:09:36 : Initial processing of species 1 complete
2019-12-12 18:09:40 : Connected putatitive homologs
2019-12-12 18:09:40 : Written final scores for species 2 to graph file
2019-12-12 18:09:40 : Written final scores for species 3 to graph file
2019-12-12 18:09:40 : Written final scores for species 1 to graph file
2019-12-12 18:09:40 : Written final scores for species 0 to graph file
2019-12-12 18:09:40 : Ran MCL

Writing orthogroups to file
---------------------------
Orthogroups have been written to tab-delimited files:
   /Users/daviddiaz/Downloads/test/Results_Dec12/Orthogroups.csv
   /Users/daviddiaz/Downloads/test/Results_Dec12/Orthogroups.txt (OrthoMCL format)
   /Users/daviddiaz/Downloads/test/Results_Dec12/Orthogroups_UnassignedGenes.csv
2019-12-12 18:09:40 : Done orthogroups

Analysing Orthogroups
=====================

Calculating gene distances
--------------------------
2019-12-12 18:09:42 : Done

Inferring gene and species trees
--------------------------------
2019-12-12 18:09:42 : Done 0 of 314
2019-12-12 18:09:43 : Done 100 of 314
2019-12-12 18:09:43 : Done 200 of 314
2019-12-12 18:09:43 : Done 300 of 314

280 trees had all species present and will be used by STAG to infer the species tree

Best outgroup(s) for species tree
---------------------------------
2019-12-12 18:09:48 : Starting STRIDE
2019-12-12 18:09:48 : Done STRIDE
Observed 4 well-supported, non-terminal duplications. 4 support the best root and 0 contradict it.
Best outgroup for species tree:
  Mycoplasma_agalactiae, Mycoplasma_hyopneumoniae

Reconciling gene trees and species tree
---------------------------------------
Outgroup: Mycoplasma_agalactiae, Mycoplasma_hyopneumoniae
2019-12-12 18:09:48 : Starting Recon and orthologues
2019-12-12 18:09:48 : Starting OF Orthologues
2019-12-12 18:09:48 : Done 0 of 314
2019-12-12 18:09:49 : Done 100 of 314
2019-12-12 18:09:49 : Done 200 of 314
2019-12-12 18:09:49 : Done 300 of 314
2019-12-12 18:09:49 : Done OF Orthologues
2019-12-12 18:09:49 : Done Recon

Writing results files
=====================
2019-12-12 18:09:49 : Done orthologues
Orthogroups have been written to tab-delimited files:
   /Users/daviddiaz/Downloads/test/Results_Dec12/Orthogroups.csv
   /Users/daviddiaz/Downloads/test/Results_Dec12/Orthogroups.txt (OrthoMCL format)
   /Users/daviddiaz/Downloads/test/Results_Dec12/Orthogroups_UnassignedGenes.csv

Gene trees:
   /Users/daviddiaz/Downloads/test/Results_Dec12/Orthologues_Dec12/Gene_Trees/

Rooted species tree:
   /Users/daviddiaz/Downloads/test/Results_Dec12/Orthologues_Dec12/SpeciesTree_rooted.txt

Species-by-species orthologues:
   /Users/daviddiaz/Downloads/test/Results_Dec12/Orthologues_Dec12/Orthologues/

Orthogroup statistics:
   Statistics_PerSpecies.csv   Statistics_Overall.csv   Orthogroups_SpeciesOverlaps.csv

OrthoFinder assigned 1938 genes (70.9% of total) to 536 orthogroups. Fifty percent of all genes were in orthogroups with 4 or more genes (G50 was 4) and were contained in the largest 299 orthogroups (O50 was 299). There were 280 orthogroups with all species present and 254 of these consisted entirely of single-copy genes.

CITATION:
 When publishing work that uses OrthoFinder please cite:
 Emms D.M. & Kelly S. (2015), Genome Biology 16:157

 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

I also try source with the same issues, no matter the path

However, I realized that the run that actually worked, it is not the same as the example results in the tutorial file

Example Results File

image

Latest run

image

It also happens if I force diamond

OrthoFinder version 2.2.6 Copyright (C) 2014 David Emms

4 thread(s) for highly parallel tasks (BLAST searches etc.)
4 thread(s) for OrthoFinder algorithm

Checking required programs are installed
----------------------------------------
Test can run "mcl -h" - ok
Test can run "fastme -i /Users/dds/Downloads/primary_transcripts/SimpleTest.phy -o /Users/dds/Downloads/primary_transcripts/SimpleTest.tre" - ok

Dividing up work for BLAST for parallel processing
--------------------------------------------------
2019-12-12 12:31:25 : Creating diamond database 1 of 6
2019-12-12 12:31:27 : Creating diamond database 2 of 6
2019-12-12 12:31:27 : Creating diamond database 3 of 6
2019-12-12 12:31:28 : Creating diamond database 4 of 6
2019-12-12 12:31:29 : Creating diamond database 5 of 6
2019-12-12 12:31:30 : Creating diamond database 6 of 6

Running diamond all-versus-all
------------------------------
Using 4 thread(s)
2019-12-12 12:31:31 : This may take some time....
2019-12-12 12:31:31 : Done 0 of 36
2019-12-12 12:42:01 : Done 10 of 36
2019-12-12 12:50:20 : Done 20 of 36
2019-12-12 12:55:50 : Done 30 of 36

Running OrthoFinder algorithm
-----------------------------
2019-12-12 12:58:39 : Initial processing of each species
2019-12-12 12:58:54 : Initial processing of species 1 complete
2019-12-12 12:59:11 : Initial processing of species 3 complete
2019-12-12 12:59:11 : Initial processing of species 2 complete
2019-12-12 12:59:22 : Initial processing of species 4 complete
2019-12-12 12:59:22 : Initial processing of species 0 complete
2019-12-12 12:59:37 : Initial processing of species 5 complete
2019-12-12 12:59:47 : Connected putatitive homologs
2019-12-12 12:59:51 : Written final scores for species 1 to graph file
2019-12-12 12:59:53 : Written final scores for species 3 to graph file
2019-12-12 12:59:54 : Written final scores for species 2 to graph file
2019-12-12 12:59:55 : Written final scores for species 0 to graph file
2019-12-12 12:59:56 : Written final scores for species 4 to graph file
2019-12-12 12:59:58 : Written final scores for species 5 to graph file
[mcl] cut <8> instances of overlap
2019-12-12 13:00:12 : Ran MCL

Writing orthogroups to file
---------------------------
Orthogroups have been written to tab-delimited files:
   /Users/dds/Downloads/primary_transcripts/Results_Dec12_3/Orthogroups.csv
   /Users/dds/Downloads/primary_transcripts/Results_Dec12_3/Orthogroups.txt (OrthoMCL format)
   /Users/dds/Downloads/primary_transcripts/Results_Dec12_3/Orthogroups_UnassignedGenes.csv
2019-12-12 13:00:15 : Done orthogroups

Analysing Orthogroups
=====================

Calculating gene distances
--------------------------
2019-12-12 13:01:17 : Done

Inferring gene and species trees
--------------------------------
2019-12-12 13:01:19 : Done 0 of 12442
2019-12-12 13:01:25 : Done 1000 of 12442
2019-12-12 13:01:31 : Done 2000 of 12442
2019-12-12 13:01:37 : Done 3000 of 12442
2019-12-12 13:01:43 : Done 4000 of 12442
2019-12-12 13:01:49 : Done 5000 of 12442
2019-12-12 13:01:55 : Done 6000 of 12442
2019-12-12 13:02:01 : Done 7000 of 12442
2019-12-12 13:02:06 : Done 8000 of 12442
2019-12-12 13:02:13 : Done 9000 of 12442
2019-12-12 13:02:19 : Done 10000 of 12442
2019-12-12 13:02:25 : Done 11000 of 12442
2019-12-12 13:02:31 : Done 12000 of 12442

5525 trees had all species present and will be used by STAG to infer the species tree

Best outgroup(s) for species tree
---------------------------------
2019-12-12 13:04:32 : Starting STRIDE
2019-12-12 13:04:35 : Done STRIDE
Observed 1101 well-supported, non-terminal duplications. 1101 support the best root and 0 contradict it.
Best outgroup for species tree:
  Drosophila_melanogaster

Reconciling gene trees and species tree
---------------------------------------
Outgroup: Drosophila_melanogaster
2019-12-12 13:04:35 : Starting Recon and orthologues
2019-12-12 13:04:35 : Starting OF Orthologues
2019-12-12 13:04:36 : Done 0 of 12442
2019-12-12 13:04:54 : Done 1000 of 12442
2019-12-12 13:05:02 : Done 2000 of 12442
2019-12-12 13:05:08 : Done 3000 of 12442
2019-12-12 13:05:13 : Done 4000 of 12442
2019-12-12 13:05:18 : Done 5000 of 12442
2019-12-12 13:05:23 : Done 6000 of 12442
2019-12-12 13:05:27 : Done 7000 of 12442
2019-12-12 13:05:31 : Done 8000 of 12442
2019-12-12 13:05:35 : Done 9000 of 12442
2019-12-12 13:05:39 : Done 10000 of 12442
2019-12-12 13:05:43 : Done 11000 of 12442
2019-12-12 13:05:46 : Done 12000 of 12442
2019-12-12 13:05:47 : Done OF Orthologues
2019-12-12 13:05:47 : Done Recon

Writing results files
=====================
2019-12-12 13:05:49 : Done orthologues
Orthogroups have been written to tab-delimited files:
   /Users/dds/Downloads/primary_transcripts/Results_Dec12_3/Orthogroups.csv
   /Users/dds/Downloads/primary_transcripts/Results_Dec12_3/Orthogroups.txt (OrthoMCL format)
   /Users/dds/Downloads/primary_transcripts/Results_Dec12_3/Orthogroups_UnassignedGenes.csv

Gene trees:
   /Users/dds/Downloads/primary_transcripts/Results_Dec12_3/Orthologues_Dec12/Gene_Trees/

Rooted species tree:
   /Users/dds/Downloads/primary_transcripts/Results_Dec12_3/Orthologues_Dec12/SpeciesTree_rooted.txt

Species-by-species orthologues:
   /Users/dds/Downloads/primary_transcripts/Results_Dec12_3/Orthologues_Dec12/Orthologues/

Orthogroup statistics:
   Statistics_PerSpecies.csv   Statistics_Overall.csv   Orthogroups_SpeciesOverlaps.csv

OrthoFinder assigned 109988 genes (83.9% of total) to 15907 orthogroups. Fifty percent of all genes were in orthogroups with 6 or more genes (G50 was 6) and were contained in the largest 5580 orthogroups (O50 was 5580). There were 5525 orthogroups with all species present and 1832 of these consisted entirely of single-copy genes.

CITATION:
 When publishing work that uses OrthoFinder please cite:
 Emms D.M. & Kelly S. (2015), Genome Biology 16:157

 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
davidemms commented 4 years ago

Hi

OrthoFinder now comes with a bin/ directory of the dependencies, does removing that change anything?

All the best David

ddiazescandon commented 4 years ago

Sorry for the late answer, I run the Source version 2.3.8 without the Bin/ folder, and it actually run but...

There is a -4 error 

OrthoFinder version 2.3.8 Copyright (C) 2014 David Emms

2019-12-16 17:06:23 : Starting OrthoFinder
8 thread(s) for highly parallel tasks (BLAST searches etc.)
1 thread(s) for OrthoFinder algorithm

Checking required programs are installed
----------------------------------------
Test can run "mcl -h" - ok
Test can run "fastme -i /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/SimpleTest.phy -o /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/SimpleTest.tre" - ok

Dividing up work for BLAST for parallel processing
--------------------------------------------------
2019-12-16 17:06:23 : Creating diamond database 1 of 4
2019-12-16 17:06:23 : Creating diamond database 2 of 4
2019-12-16 17:06:23 : Creating diamond database 3 of 4
2019-12-16 17:06:23 : Creating diamond database 4 of 4

Running diamond all-versus-all
------------------------------
Using 8 thread(s)
2019-12-16 17:06:23 : This may take some time....
2019-12-16 17:06:23 : Done 0 of 16

ERROR: external program called by OrthoFinder returned an error code: -4

Command: diamond blastp -d /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/diamondDBSpecies3 -q /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/Species0.fa -o /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/Blast0_3.txt --more-sensitive -p 1 --quiet -e 0.001 --compress 1

stdout
------
b''
stderr
------
b'diamond v0.9.29.130 | by Benjamin Buchfink <buchfink@gmail.com>\nLicensed under the GNU GPL <https://www.gnu.org/licenses/gpl.txt>\nCheck http://github.com/bbuchfink/diamond for updates.\n\n'

ERROR: external program called by OrthoFinder returned an error code: -4

Command: diamond blastp -d /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/diamondDBSpecies1 -q /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/Species3.fa -o /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/Blast3_1.txt --more-sensitive -p 1 --quiet -e 0.001 --compress 1

stdout
------
b''
stderr
------
b'diamond v0.9.29.130 | by Benjamin Buchfink <buchfink@gmail.com>\nLicensed under the GNU GPL <https://www.gnu.org/licenses/gpl.txt>\nCheck http://github.com/bbuchfink/diamond for updates.\n\n'

ERROR: external program called by OrthoFinder returned an error code: -4

Command: diamond blastp -d /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/diamondDBSpecies1 -q /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/Species1.fa -o /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/Blast1_1.txt --more-sensitive -p 1 --quiet -e 0.001 --compress 1

stdout
------
b''
stderr
------
b'diamond v0.9.29.130 | by Benjamin Buchfink <buchfink@gmail.com>\nLicensed under the GNU GPL <https://www.gnu.org/licenses/gpl.txt>\nCheck http://github.com/bbuchfink/diamond for updates.\n\n'

ERROR: external program called by OrthoFinder returned an error code: -4

Command: diamond blastp -d /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/diamondDBSpecies0 -q /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/Species1.fa -o /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/Blast1_0.txt --more-sensitive -p 1 --quiet -e 0.001 --compress 1

stdout
------
b''
stderr
------
b'diamond v0.9.29.130 | by Benjamin Buchfink <buchfink@gmail.com>\nLicensed under the GNU GPL <https://www.gnu.org/licenses/gpl.txt>\nCheck http://github.com/bbuchfink/diamond for updates.\n\n'

ERROR: external program called by OrthoFinder returned an error code: -4

Command: diamond blastp -d /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/diamondDBSpecies3 -q /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/Species1.fa -o /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/Blast1_3.txt --more-sensitive -p 1 --quiet -e 0.001 --compress 1

stdout
------
b''
stderr
------
b'diamond v0.9.29.130 | by Benjamin Buchfink <buchfink@gmail.com>\nLicensed under the GNU GPL <https://www.gnu.org/licenses/gpl.txt>\nCheck http://github.com/bbuchfink/diamond for updates.\n\n'

ERROR: external program called by OrthoFinder returned an error code: -4

Command: diamond blastp -d /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/diamondDBSpecies0 -q /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/Species3.fa -o /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/Blast3_0.txt --more-sensitive -p 1 --quiet -e 0.001 --compress 1

stdout
------
b''
stderr
------
b'diamond v0.9.29.130 | by Benjamin Buchfink <buchfink@gmail.com>\nLicensed under the GNU GPL <https://www.gnu.org/licenses/gpl.txt>\nCheck http://github.com/bbuchfink/diamond for updates.\n\n'

ERROR: external program called by OrthoFinder returned an error code: -4

Command: diamond blastp -d /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/diamondDBSpecies0 -q /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/Species0.fa -o /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/Blast0_0.txt --more-sensitive -p 1 --quiet -e 0.001 --compress 1

stdout
------
b''
stderr
------
b'diamond v0.9.29.130 | by Benjamin Buchfink <buchfink@gmail.com>\nLicensed under the GNU GPL <https://www.gnu.org/licenses/gpl.txt>\nCheck http://github.com/bbuchfink/diamond for updates.\n\n'

ERROR: external program called by OrthoFinder returned an error code: -4

Command: diamond blastp -d /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/diamondDBSpecies1 -q /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/Species0.fa -o /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/Blast0_1.txt --more-sensitive -p 1 --quiet -e 0.001 --compress 1

stdout
------
b''
stderr
------
b'diamond v0.9.29.130 | by Benjamin Buchfink <buchfink@gmail.com>\nLicensed under the GNU GPL <https://www.gnu.org/licenses/gpl.txt>\nCheck http://github.com/bbuchfink/diamond for updates.\n\n'

ERROR: external program called by OrthoFinder returned an error code: -4

Command: diamond blastp -d /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/diamondDBSpecies2 -q /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/Species3.fa -o /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/Blast3_2.txt --more-sensitive -p 1 --quiet -e 0.001 --compress 1

stdout
------
b''
stderr
------
b'diamond v0.9.29.130 | by Benjamin Buchfink <buchfink@gmail.com>\nLicensed under the GNU GPL <https://www.gnu.org/licenses/gpl.txt>\nCheck http://github.com/bbuchfink/diamond for updates.\n\n'

ERROR: external program called by OrthoFinder returned an error code: -4

Command: diamond blastp -d /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/diamondDBSpecies2 -q /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/Species1.fa -o /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/Blast1_2.txt --more-sensitive -p 1 --quiet -e 0.001 --compress 1

stdout
------
b''
stderr
------
b'diamond v0.9.29.130 | by Benjamin Buchfink <buchfink@gmail.com>\nLicensed under the GNU GPL <https://www.gnu.org/licenses/gpl.txt>\nCheck http://github.com/bbuchfink/diamond for updates.\n\n'

ERROR: external program called by OrthoFinder returned an error code: -4

Command: diamond blastp -d /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/diamondDBSpecies0 -q /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/Species2.fa -o /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/Blast2_0.txt --more-sensitive -p 1 --quiet -e 0.001 --compress 1

stdout
------
b''
stderr
------
b'diamond v0.9.29.130 | by Benjamin Buchfink <buchfink@gmail.com>\nLicensed under the GNU GPL <https://www.gnu.org/licenses/gpl.txt>\nCheck http://github.com/bbuchfink/diamond for updates.\n\n'

ERROR: external program called by OrthoFinder returned an error code: -4

Command: diamond blastp -d /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/diamondDBSpecies2 -q /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/Species0.fa -o /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/Blast0_2.txt --more-sensitive -p 1 --quiet -e 0.001 --compress 1

stdout
------
b''
stderr
------
b'diamond v0.9.29.130 | by Benjamin Buchfink <buchfink@gmail.com>\nLicensed under the GNU GPL <https://www.gnu.org/licenses/gpl.txt>\nCheck http://github.com/bbuchfink/diamond for updates.\n\n'

ERROR: external program called by OrthoFinder returned an error code: -4

Command: diamond blastp -d /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/diamondDBSpecies3 -q /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/Species3.fa -o /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/Blast3_3.txt --more-sensitive -p 1 --quiet -e 0.001 --compress 1

stdout
------
b''
stderr
------
b'diamond v0.9.29.130 | by Benjamin Buchfink <buchfink@gmail.com>\nLicensed under the GNU GPL <https://www.gnu.org/licenses/gpl.txt>\nCheck http://github.com/bbuchfink/diamond for updates.\n\n'

ERROR: external program called by OrthoFinder returned an error code: -4

Command: diamond blastp -d /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/diamondDBSpecies1 -q /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/Species2.fa -o /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/Blast2_1.txt --more-sensitive -p 1 --quiet -e 0.001 --compress 1

stdout
------
b''
stderr
------
b'diamond v0.9.29.130 | by Benjamin Buchfink <buchfink@gmail.com>\nLicensed under the GNU GPL <https://www.gnu.org/licenses/gpl.txt>\nCheck http://github.com/bbuchfink/diamond for updates.\n\n'

ERROR: external program called by OrthoFinder returned an error code: -4

Command: diamond blastp -d /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/diamondDBSpecies2 -q /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/Species2.fa -o /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/Blast2_2.txt --more-sensitive -p 1 --quiet -e 0.001 --compress 1

stdout
------
b''
stderr
------
b'diamond v0.9.29.130 | by Benjamin Buchfink <buchfink@gmail.com>\nLicensed under the GNU GPL <https://www.gnu.org/licenses/gpl.txt>\nCheck http://github.com/bbuchfink/diamond for updates.\n\n'

ERROR: external program called by OrthoFinder returned an error code: -4

Command: diamond blastp -d /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/diamondDBSpecies3 -q /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/Species2.fa -o /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/Blast2_3.txt --more-sensitive -p 1 --quiet -e 0.001 --compress 1

stdout
------
b''
stderr
------
b'diamond v0.9.29.130 | by Benjamin Buchfink <buchfink@gmail.com>\nLicensed under the GNU GPL <https://www.gnu.org/licenses/gpl.txt>\nCheck http://github.com/bbuchfink/diamond for updates.\n\n'
2019-12-16 17:06:25 : Done all-versus-all sequence search

Running OrthoFinder algorithm
-----------------------------
2019-12-16 17:06:25 : Initial processing of each species
WARNING: Too few hits between species 0 and species 0 to normalise the scores, these hits will be ignored
WARNING: Too few hits between species 0 and species 1 to normalise the scores, these hits will be ignored
WARNING: Too few hits between species 0 and species 2 to normalise the scores, these hits will be ignored
WARNING: Too few hits between species 0 and species 3 to normalise the scores, these hits will be ignored
2019-12-16 17:06:25 : Initial processing of species 0 complete
WARNING: Too few hits between species 1 and species 0 to normalise the scores, these hits will be ignored
WARNING: Too few hits between species 1 and species 1 to normalise the scores, these hits will be ignored
WARNING: Too few hits between species 1 and species 2 to normalise the scores, these hits will be ignored
WARNING: Too few hits between species 1 and species 3 to normalise the scores, these hits will be ignored
2019-12-16 17:06:25 : Initial processing of species 1 complete
WARNING: Too few hits between species 2 and species 0 to normalise the scores, these hits will be ignored
WARNING: Too few hits between species 2 and species 1 to normalise the scores, these hits will be ignored
WARNING: Too few hits between species 2 and species 2 to normalise the scores, these hits will be ignored
WARNING: Too few hits between species 2 and species 3 to normalise the scores, these hits will be ignored
2019-12-16 17:06:25 : Initial processing of species 2 complete
WARNING: Too few hits between species 3 and species 0 to normalise the scores, these hits will be ignored
WARNING: Too few hits between species 3 and species 1 to normalise the scores, these hits will be ignored
WARNING: Too few hits between species 3 and species 2 to normalise the scores, these hits will be ignored
WARNING: Too few hits between species 3 and species 3 to normalise the scores, these hits will be ignored
2019-12-16 17:06:26 : Initial processing of species 3 complete
2019-12-16 17:06:28 : Connected putative homologues
2019-12-16 17:06:28 : Written final scores for species 0 to graph file
2019-12-16 17:06:28 : Written final scores for species 1 to graph file
2019-12-16 17:06:28 : Written final scores for species 2 to graph file
2019-12-16 17:06:28 : Written final scores for species 3 to graph file
2019-12-16 17:06:29 : Ran MCL

Writing orthogroups to file
---------------------------
/Users/daviddiaz/opt/anaconda3/lib/python3.7/site-packages/numpy/core/fromnumeric.py:3257: RuntimeWarning: Mean of empty slice.
  out=out, **kwargs)
/Users/daviddiaz/opt/anaconda3/lib/python3.7/site-packages/numpy/core/_methods.py:161: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
Traceback (most recent call last):
  File "/Users/daviddiaz/Desktop/TEST/OrthoFinder_source/orthofinder.py", line 7, in <module>
    main(args)
  File "/Users/daviddiaz/Desktop/TEST/OrthoFinder_source/scripts_of/__main__.py", line 1678, in main
    DoOrthogroups(options, speciesInfoObj, seqsInfo)    
  File "/Users/daviddiaz/Desktop/TEST/OrthoFinder_source/scripts_of/__main__.py", line 1353, in DoOrthogroups
    Stats(ogs, speciesNamesDict, speciesInfoObj.speciesToUse, files.FileHandler.iResultsVersion)
  File "/Users/daviddiaz/Desktop/TEST/OrthoFinder_source/scripts_of/__main__.py", line 731, in Stats
    j, _ = next((i, x) for i, x in enumerate(L) if x > nAssigned/2)
StopIteration
ddiazescandon commented 4 years ago

It runs fine with -S mmseq, and deleting the bin folder, I will try it in the Conda version.

OrthoFinder version 2.3.8 Copyright (C) 2014 David Emms

2019-12-16 17:35:57 : Starting OrthoFinder
8 thread(s) for highly parallel tasks (BLAST searches etc.)
1 thread(s) for OrthoFinder algorithm

Checking required programs are installed
----------------------------------------
Test can run "mcl -h" - ok
Test can run "fastme -i /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16_3/WorkingDirectory/SimpleTest.phy -o /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16_3/WorkingDirectory/SimpleTest.tre" - ok

Dividing up work for BLAST for parallel processing
--------------------------------------------------
2019-12-16 17:36:02 : Creating mmseqs database 1 of 4
2019-12-16 17:36:05 : Creating mmseqs database 2 of 4
2019-12-16 17:36:08 : Creating mmseqs database 3 of 4
2019-12-16 17:36:12 : Creating mmseqs database 4 of 4

Running mmseqs all-versus-all
-----------------------------
Using 8 thread(s)
2019-12-16 17:36:15 : This may take some time....
2019-12-16 17:36:15 : Done 0 of 16
2019-12-16 17:36:37 : Done all-versus-all sequence search

Running OrthoFinder algorithm
-----------------------------
2019-12-16 17:36:37 : Initial processing of each species
2019-12-16 17:36:37 : Initial processing of species 0 complete
2019-12-16 17:36:37 : Initial processing of species 1 complete
2019-12-16 17:36:37 : Initial processing of species 2 complete
2019-12-16 17:36:38 : Initial processing of species 3 complete
2019-12-16 17:36:40 : Connected putative homologues
2019-12-16 17:36:40 : Written final scores for species 0 to graph file
2019-12-16 17:36:40 : Written final scores for species 1 to graph file
2019-12-16 17:36:40 : Written final scores for species 2 to graph file
2019-12-16 17:36:40 : Written final scores for species 3 to graph file
2019-12-16 17:36:41 : Ran MCL

Writing orthogroups to file
---------------------------
OrthoFinder assigned 2135 genes (78.1% of total) to 585 orthogroups. Fifty percent of all genes were in orthogroups with 4 or more genes (G50 was 4) and were contained in the largest 281 orthogroups (O50 was 281). There were 260 orthogroups with all species present and 237 of these consisted entirely of single-copy genes.

2019-12-16 17:36:42 : Done orthogroups

Analysing Orthogroups
=====================

Calculating gene distances
--------------------------
2019-12-16 17:36:45 : Done

Inferring gene and species trees
--------------------------------
2019-12-16 17:36:46 : Done 0 of 315
2019-12-16 17:36:46 : Done 100 of 315
2019-12-16 17:36:46 : Done 200 of 315
2019-12-16 17:36:47 : Done 300 of 315

260 trees had all species present and will be used by STAG to infer the species tree

Best outgroup(s) for species tree
---------------------------------
2019-12-16 17:36:55 : Starting STRIDE
2019-12-16 17:36:56 : Done STRIDE
Observed 2 well-supported, non-terminal duplications. 2 support the best roots and 0 contradict them.
Best outgroups for species tree:
  Mycoplasma_hyopneumoniae
  Mycoplasma_hyopneumoniae, Mycoplasma_agalactiae
  Mycoplasma_agalactiae

WARNING: Multiple potential species tree roots were identified, only one will be analyed.

Reconciling gene trees and species tree
---------------------------------------
Outgroup: Mycoplasma_hyopneumoniae
2019-12-16 17:36:56 : Starting Recon and orthologues
2019-12-16 17:36:56 : Starting OF Orthologues
2019-12-16 17:36:56 : Done 0 of 315
2019-12-16 17:36:57 : Done 100 of 315
2019-12-16 17:36:57 : Done 200 of 315
2019-12-16 17:36:58 : Done 300 of 315
2019-12-16 17:36:58 : Done OF Orthologues
2019-12-16 17:36:58 : Done Recon

Writing results files
=====================
2019-12-16 17:36:58 : Done orthologues

Results:
    /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16_3/

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
(base) Davids-MacBook-Pro:~ daviddiaz$
davidemms commented 4 years ago

Hi

The warning message about DIAMOND is fine, it's just printing out a message:

diamond v0.9.29.130 | by Benjamin Buchfink <buchfink@gmail.com>\nLicensed under the GNU GPL <https://www.gnu.org/licenses/gpl.txt>\nCheck http://github.com/bbuchfink/diamond for updates.

OrthoFinder reported this because diamond printed it to stderr and so there was the potential that something was wrong. I've submitted a change recently so that OrthoFinder ignores this.

The error code of -4 is more troubling. I'm not sure what this is. Could you try running one of the commands that OrthoFinder said it ran and see what happens e.g. diamond blastp -d /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/diamondDBSpecies3 -q /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/Species3.fa -o /Users/daviddiaz/Desktop/TEST/OrthoFinder_source/ExampleData/OrthoFinder/Results_Dec16/WorkingDirectory/Blast3_3.txt --more-sensitive -p 1 --quiet -e 0.001 --compress 1

What are the messages diamond prints? Does the result file look of (e.g. compared to the file created by MMseqs). Given that OrthoFinder is printing a message saying e.g. "Too few hits between species 0 and species 0", and with the error code of -4 from diaomond, it suggests something is going wrong with DIAMOND on your machine.

All the best David

desmondramirez commented 4 years ago

Hi David and David,

Deleting the bin directory either from the condo installation or source install of 2.3.8 doesn't change anything, even though all the dependencies are already installed and in the path (as far as I can tell).

I can run 2.3.3 from source, which is what I did, but ideally I'd like to be able to run the newest version of the software!! I'm on MacOS, so I don't know if that has something to do with it also.

Des

desmondramirez commented 4 years ago

Oops, slight edit, ran orthofinder 2.3.3 through docker. That worked. But now I'd like to add another species and am running into trouble. As a kludge I'll probably rerun the whole analysis including the species I wanted to add.

davidemms commented 4 years ago

Hi Des

It may have something to do with it but I'm finding it hard to think what the problem could be. With the bin directory deleted, could you open up a terminal, type "which diamond" then try and run OrthoFinder on the ExampleDataset and paste the whole terminal output from both of the commands here.

Thanks David

ddiazescandon commented 4 years ago 
diamond v0.9.29.130 | by Benjamin Buchfink <buchfink@gmail.com>
Licensed under the GNU GPL <https://www.gnu.org/licenses/gpl.txt>
Check http://github.com/bbuchfink/diamond for updates.

Illegal instruction: 4
desmondramirez commented 4 years ago

Hi David,

Here's the MacOS trial. I deleted the bin directory in miniconda3/pkgs/orthofinder, then tried to Run OrthoFinder:

(base) ➜  OrthoFinder which diamond
/Users/desmondramirez/miniconda3/bin/diamond
(base) ➜  OrthoFinder orthofinder -f ExampleData 

OrthoFinder version 2.3.8 Copyright (C) 2014 David Emms

2019-12-17 13:46:24 : Starting OrthoFinder
12 thread(s) for highly parallel tasks (BLAST searches etc.)
1 thread(s) for OrthoFinder algorithm

Checking required programs are installed
----------------------------------------

ERROR: Cannot run diamond
Format of make database command:
  diamond makedb --in INPUT -d OUTPUT
ERROR: Cannot run diamond
Format of search database command:
  diamond blastp -d DATABASE -q INPUT -o OUTPUT --more-sensitive -p 1 --quiet -e 0.001 --compress 1
Please check diamond is installed and that the executables are in the system path

ERROR: An error occurred, please review error messages for more information.
desmondramirez commented 4 years ago

Here's the error I get trying to run OrthoFinder on my campus computing cluster:

(base) [dr34a@ghpcc06 OrthoFinder]$ orthofinder -f ExampleData/

OrthoFinder version 2.3.8 Copyright (C) 2014 David Emms

2019-12-17 13:51:39 : Starting OrthoFinder
32 thread(s) for highly parallel tasks (BLAST searches etc.)
1 thread(s) for OrthoFinder algorithm

Checking required programs are installed
----------------------------------------
Test can run "mcl -h" - failed

stdout:

stderr:
b"mcl: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by mcl)\n"
ERROR: Cannot run MCL with the command "mcl -h"
Please check MCL is installed and in the system path

ERROR: An error occurred, please review error messages for more information.
(base) [dr34a@ghpcc06 OrthoFinder]$ ./orthofinder -f ExampleData/
./orthofinder: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /tmp/_MEIJcCFwX/libz.so.1)
(base) [dr34a@ghpcc06 OrthoFinder]$ which orthofinder
/project/uma_paul_katz/software/miniconda/bin/orthofinder
(base) [dr34a@ghpcc06 OrthoFinder]$ which mcl
/project/uma_paul_katz/software/miniconda/bin/mcl
(base) [dr34a@ghpcc06 OrthoFinder]$ which diamond
/project/uma_paul_katz/software/miniconda/bin/diamond
ddiazescandon commented 4 years ago

Try downloading the source file instead, delete the bin folder and call the orthofinder.py, It worked for me, and I have exactly the same issue, and probably the diamond error is going to happen so switch to -S mmseq or blast

desmondramirez commented 4 years ago

Thank both of you.

@ddiazescandon I tried as you suggested, now orthofinder runs using diamond without any errors on MacOS. I did manually install all of the dependencies with conda beforehand.

(base) ➜  OrthoFinder-2.3.8 python orthofinder.py -f ExampleDataset

OrthoFinder version 2.3.8 Copyright (C) 2014 David Emms

2019-12-17 14:03:31 : Starting OrthoFinder
12 thread(s) for highly parallel tasks (BLAST searches etc.)
1 thread(s) for OrthoFinder algorithm

Checking required programs are installed
----------------------------------------
Test can run "mcl -h" - ok
Test can run "fastme -i /Users/desmondramirez/Downloads/OrthoFinder-2.3.8/ExampleDataset/OrthoFinder/Results_Dec17_1/WorkingDirectory/SimpleTest.phy -o /Users/desmondramirez/Downloads/OrthoFinder-2.3.8/ExampleDataset/OrthoFinder/Results_Dec17_1/WorkingDirectory/SimpleTest.tre" - ok

Dividing up work for BLAST for parallel processing
--------------------------------------------------
2019-12-17 14:03:31 : Creating diamond database 1 of 4
2019-12-17 14:03:31 : Creating diamond database 2 of 4
2019-12-17 14:03:31 : Creating diamond database 3 of 4
2019-12-17 14:03:31 : Creating diamond database 4 of 4

Running diamond all-versus-all
------------------------------
Using 12 thread(s)
2019-12-17 14:03:31 : This may take some time....
2019-12-17 14:03:31 : Done 0 of 16
2019-12-17 14:03:37 : Done all-versus-all sequence search

Running OrthoFinder algorithm
-----------------------------
2019-12-17 14:03:37 : Initial processing of each species
2019-12-17 14:03:37 : Initial processing of species 0 complete
2019-12-17 14:03:38 : Initial processing of species 1 complete
2019-12-17 14:03:38 : Initial processing of species 2 complete
2019-12-17 14:03:38 : Initial processing of species 3 complete
2019-12-17 14:03:40 : Connected putative homologues
2019-12-17 14:03:40 : Written final scores for species 0 to graph file
2019-12-17 14:03:40 : Written final scores for species 1 to graph file
2019-12-17 14:03:40 : Written final scores for species 2 to graph file
2019-12-17 14:03:40 : Written final scores for species 3 to graph file
2019-12-17 14:03:40 : Ran MCL

Writing orthogroups to file
---------------------------
OrthoFinder assigned 2202 genes (80.6% of total) to 604 orthogroups. Fifty percent of all genes were in orthogroups with 4 or more genes (G50 was 4) and were contained in the largest 281 orthogroups (O50 was 281). There were 269 orthogroups with all species present and 246 of these consisted entirely of single-copy genes.

2019-12-17 14:03:41 : Done orthogroups

Analysing Orthogroups
=====================

Calculating gene distances
--------------------------
2019-12-17 14:03:43 : Done

Inferring gene and species trees
--------------------------------
2019-12-17 14:03:43 : Done 0 of 325
2019-12-17 14:03:43 : Done 100 of 325
2019-12-17 14:03:44 : Done 200 of 325
2019-12-17 14:03:44 : Done 300 of 325

269 trees had all species present and will be used by STAG to infer the species tree

Best outgroup(s) for species tree
---------------------------------
2019-12-17 14:03:48 : Starting STRIDE
2019-12-17 14:03:49 : Done STRIDE
Observed 2 well-supported, non-terminal duplications. 2 support the best roots and 0 contradict them.
Best outgroups for species tree:
  Mycoplasma_hyopneumoniae
  Mycoplasma_gallisepticum, Mycoplasma_genitalium
  Mycoplasma_agalactiae

WARNING: Multiple potential species tree roots were identified, only one will be analyed.

Reconciling gene trees and species tree
---------------------------------------
Outgroup: Mycoplasma_hyopneumoniae
2019-12-17 14:03:49 : Starting Recon and orthologues
2019-12-17 14:03:49 : Starting OF Orthologues
2019-12-17 14:03:49 : Done 0 of 325
2019-12-17 14:03:49 : Done 100 of 325
2019-12-17 14:03:49 : Done 200 of 325
2019-12-17 14:03:49 : Done 300 of 325
2019-12-17 14:03:49 : Done OF Orthologues
2019-12-17 14:03:49 : Done Recon

Writing results files
=====================
2019-12-17 14:03:49 : Done orthologues

Results:
    /Users/desmondramirez/Downloads/OrthoFinder-2.3.8/ExampleDataset/OrthoFinder/Results_Dec17_1/

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
katier239 commented 4 years ago

Hi all,

I've also been getting the same error message

ERROR: external program called by OrthoFinder returned an error code: -4

I’m not certain what causes this, but after having a dig around some help forums, I suspect it may be due to the diamond dependency included with the current conda install of OrthoFinder not being fully compatible with certain macOS (I’m using High Sierra).

I did the following and was then able to get the example analysis to run successfully:

1) Search for all files/folders associated with OrthoFinder and delete them

2) Install diamond from source code as per the diamond manual (after first using homebrew to install cmake). 

wget http://github.com/bbuchfink/diamond/archive/v0.9.29.tar.gz

tar xzf v0.9.29.tar.gz

cd  diamond-0.9.29

mkdir bin

cd bin

cmake

make install

3) Re-install OrthoFinder using conda.

4) Delete the bin folder as described in the earlier post above, and and extra conda-installed diamond files

5) Run the example analysis

See also: https://stackoverflow.com/questions/14268887/what-is-the-illegal-instruction-4-error-and-why-does-mmacosx-version-min-10

http://www.diamondsearch.org/index.php?threads/diamond-not-working-on-mac.65/#post-147

Note: The diamond installation failed when I tried to install by cloning the git repository, as suggested in the above webpage, but worked ok when I dowloaded the tarball using wget, as per the manual. I got a fair few warning messages during the make install step, but as the example analysis seemed to run ok, I am hoping the warnings are not a problem

davidemms commented 4 years ago

Hi

This sounds like it could be a problem with the bioconda diamond recipe, thanks for all your work tracking this down. I will look into trying to get the recipe updated since your second link suggests that the issue has just been fixed in diamond.

All the best David

LovellHAGSC commented 4 years ago

It also appears to not be able to find MCL ... so, not a problem specific to diamond.

davidemms commented 4 years ago

I think that this issue is the same set of issues as those in https://github.com/davidemms/OrthoFinder/issues/328 and https://github.com/davidemms/OrthoFinder/issues/341. I think these are resolved now and the latest version of OrthoFinder, which is now on bioconda, should resolve all these issues. If anyone still has any of these issues with the latest version then please report it here or in a new issue.

To sumarise, I think there were a few issues which all caused problems, particularly on Mac using bioconda:

All the best David