Comments (5)
Best solution is to just mask the version of diamond distributed with anaconda and supply your own. I don't know who is updating the anaconda distribution, but I might recommend updating the version of diamond supplied with it.
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Hello? Can you tell me in detail how to solve the problem when Diamand cannot be used? Thank you vary much!
from orthofinder.
Hello? Can you tell me in detail how to solve the problem when Diamand cannot be used? Thank you vary much!
I downloaded OrthoFinder over anaconda, so it was located in a folder with a name like ~/envs/orthofinder/bin
. There should also be a program in that folder named diamond
. Rename this file to something like diamond_DEPRECATED
or delete it altogether. Then go to the diamond github page (https://github.com/bbuchfink/diamond) and download the file for your system. Then unpack the file and retrieve the diamond executable. Either put it in ~/envs/orthofinder/bin
or some other place where it will be found in your PATH
variable.
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I did this and succeeded, but there was a warning, as follows, have you ever encountered it? Thank you!
WARNING: program called by OrthoFinder produced output to stderr
Command: diamond blastp --ignore-warnings -d /mnt/share/2024.1.22/11/tri40/OrthoFinder/Results_Jan22_1/WorkingDirectory/diamondDBSpecies27 -q /mnt/share/2024.1.22/11/tri40/OrthoFinder/Results_Jan22_1/WorkingDirectory/Species36.fa -o /mnt/share/2024.1.22/11/tri40/OrthoFinder/Results_Jan22_1/WorkingDirectory/Blast36_27.txt --more-sensitive -p 1 --quiet -e 0.001 --compress 1
stdout
b''
stderr
b'Warning: Failed to delete temporary file /mnt/share/2024.1.22/11/tri40/OrthoFinder/Results_Jan22_1/WorkingDirectory/diamond-tmp-DioQLv\n'
from orthofinder.
I did this and succeeded, but there was a warning, as follows, have you ever encountered it? Thank you!
WARNING: program called by OrthoFinder produced output to stderr
Command: diamond blastp --ignore-warnings -d /mnt/share/2024.1.22/11/tri40/OrthoFinder/Results_Jan22_1/WorkingDirectory/diamondDBSpecies27 -q /mnt/share/2024.1.22/11/tri40/OrthoFinder/Results_Jan22_1/WorkingDirectory/Species36.fa -o /mnt/share/2024.1.22/11/tri40/OrthoFinder/Results_Jan22_1/WorkingDirectory/Blast36_27.txt --more-sensitive -p 1 --quiet -e 0.001 --compress 1
stdout
b''
stderr
b'Warning: Failed to delete temporary file /mnt/share/2024.1.22/11/tri40/OrthoFinder/Results_Jan22_1/WorkingDirectory/diamond-tmp-DioQLv\n'
I have not ever had that error but I don't think it's a problem. You can always delete temporary files manually if you need to.
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Related Issues (20)
- "Invalid escape sequence" errors while starting OrthoFinder HOT 1
- Hello! I have 11 .faa files in a folder. I ran orthofinder -d -f /public/home/newfasta -t 64 -o output_orthofinder. But after 13-14 minutes process failed. There is no error. I opened slurm.out file then checked. there was written like below. HOT 1
- total identical sequences clustered into one orthogroup, but the topology of gene tree divided into multiple clades HOT 1
- Species tree make_ultrameric.py not working HOT 1
- [Possible Bug] The `-og` option doesn't stop after inferring orthogroups HOT 1
- [Feature Request] Allow for passing options to Diamond and other dependencies HOT 1
- Single copy orthologs (SCO) are not being generated HOT 1
- not an issue, clarification wanted for which sequences are represented in orthogroups HOT 4
- what is the Orthogroup column in N*.tsv? HOT 1
- Question_process_Orthofinder HOT 2
- issue with running Orthofinder HOT 2
- HIV teste 1 HOT 4
- About -a option: using pre-computed BLAST results does not increase the number of orthofinder threads HOT 1
- Option to start Orthofinder at stage of inferring trees from MSAs? HOT 1
- header changed in MSA
- Diamond stuck on "Running diamond all-versus-all" HOT 1
- Option to stop Orthofinder after building the species tree? HOT 2
- Running OrthoFinder with Large Species Set (>2k) and Skipping GeneTree Construction HOT 2
- disagreement between OrthologuesStats_one-to-one.tsv and Orthogroups.GeneCount.tsv HOT 5
- Inferring remaining multiple sequence alignments and gene trees——This step has been stuck for ten days HOT 3
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