Open ld9866 opened 2 years ago
davidemms
commented
2 years ago 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
commented
2 years ago ... 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
commented
9 months ago maybe you can try to replace "." in sequences with "X" in your FASTA files. e.g. sed -i '/^>/!s/./X/g' species1.fasta
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!