diamond dropped --ignore-warnings flag, leads to error about orthofinder HOT 5 CLOSED

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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