Diamond makedb failed error in tutorial

[ld9866]

On the Orthofinder page for tutorials on the one titled "2. Running an example OrthoFinder analysis," the example files are available for download as a zip file. After downloading the tutorial files and running the following command "orthofinder -f primary_transcripts/" the tutorial states that orthofinder will run normally and provide output as described. However, OrthoFinder version 2.5.4 still cannot used according to your reply in "https://github.com/davidemms/OrthoFinder/issues/607".

stdout

b'' stderr

b'diamond v2.0.12.150 (C) Max Planck Society for the Advancement of Science\nDocumentation, support and updates available at http://www.diamondsearch.org\nPlease cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)\n\n#CPU threads: 64\nScoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)\nDatabase input file: ~/OrthoFinder/Results_Oct13/WorkingDirectory/Species0.fa\nOpening the database file... [0s]\nLoading sequences... [0.001s]\nError: The sequences are expected to be proteins but only contain DNA letters. Use the option --ignore-warnings to proceed.\n' ERROR: diamond makedb failed ERROR: An error occurred, please review the error messages they may contain useful information about the problem. Although we changed "diamond blastp -d DATABASE ......." to "diamond blastp --ignore-warnings -d DATABASE......." in ~/anaconda3/envs/orthofinder/bin/scripts_of/config.json, it still can not work!

Thank you!

[davidemms]

Hi

Could you try making a change in ~/anaconda3/envs/orthofinder/bin/scripts_of/config.json that should make the command fail immediately, e.g. "not-diamond blastp -d DATABASE ......." to ensure that the changes you are making are in the correct place and are being picked up. Let me know how you get on.

David

[davidemms]

... in fact, the error message above says the error occurs with diamond makedb, so you will have to make the change to that line to make it work:

    "db_cmd": "diamond makedb --ignore-warnings --in INPUT -d OUTPUT",

[Jefferson-Chou]

maybe you can try to replace "." in sequences with "X" in your FASTA files. e.g. sed -i '/^>/!s/./X/g' species1.fasta