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.

[timurrxxcd]

OrthoFinder version 2.5.5 Copyright (C) 2014 David Emms

2024-06-02 15:53:19 : Starting OrthoFinder 2.5.5 64 thread(s) for highly parallel tasks (BLAST searches etc.) 8 thread(s) for OrthoFinder algorithm

Checking required programs are installed

Test can run "mcl -h" - ok Test can run "fastme -i output_orthofinder/Results_Jun02/WorkingDirectory/dependencies/SimpleTest.phy -o output_orthofinder/Results_Jun02/WorkingDirectory/dependencies/SimpleTest.tre" - ok

WARNING: Files have been ignored as they don't appear to be FASTA files: slurm-15522577.out slurm-15544975.out OrthoFinder expects FASTA files to have one of the following extensions: fa, fasta, faa, fas, pep

Dividing up work for BLAST for parallel processing

2024-06-02 15:53:24 : Creating blast_nucl database 1 of 11 2024-06-02 15:53:38 : Creating blast_nucl database 2 of 11 2024-06-02 15:53:52 : Creating blast_nucl database 3 of 11 2024-06-02 15:53:55 : Creating blast_nucl database 4 of 11 2024-06-02 15:54:05 : Creating blast_nucl database 5 of 11 2024-06-02 15:54:16 : Creating blast_nucl database 6 of 11 2024-06-02 15:54:21 : Creating blast_nucl database 7 of 11 2024-06-02 15:54:45 : Creating blast_nucl database 8 of 11 2024-06-02 15:55:01 : Creating blast_nucl database 9 of 11 2024-06-02 15:55:11 : Creating blast_nucl database 10 of 11 2024-06-02 15:55:22 : Creating blast_nucl database 11 of 11

Running blast_nucl all-versus-all

Using 64 thread(s) 2024-06-02 15:55:31 : This may take some time.... 2024-06-02 15:55:32 : Done 0 of 121

WARNING: program called by OrthoFinder produced output to stderr

[davidemms]

Do you have the output to stderr that is mentioned at the end of your post?

[irislin886]

Hi, I am having the same problem too. And I did not find any output to stderr. Have you happened to fix the problem? If so, would you mind sharing how you fix the issue?

[timurrxxcd]

Hello, unfortunately I didn’t solve it. And gave up. But I know what is the problem. Problem is that, you need to retain only long and one transcript per protein. Because some proteins have same structure as they are homologous as far as I know. Then you can rerun. Good luck!

On Tue, Oct 22, 2024 at 04:53 Iris @.***> wrote:

Hi, I am having the same problem too. And I did not find any output to stderr. Have you happened to fix the problem? If so, would you mind sharing how you fix the issue?

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