I use proteinortho-v6.0.30 for detecting orthologous protein of a large dataset:
nohup proteinortho -project=protein_ortho_cluster -checkfasta -e=1e-5 -cov=50 -identity=30 -clean -cpus=50 ref_CDS_data/*.fasta > protein_cluster_information 2>&1.
The proteinortho uses diamond-v2.0.6 in my computer, and I also have tried v2.0.7 and v2.0.8, but they all give me the same error message.
What's more, I have try to run proteinortho many times, and it fails in different position, sometimes the alignment process is below 1%, sometimes 3-4%, and sometimes even 30%.
I have also try to use the -force parameter and remove all the sequences don't qualify the diamond request reported by -checkfasta parameter. But all these don't solve the problem.
There are still 200GB space in the working directory, and the computer has 256GB memory, the dataset contain 2714 bacteria genome.
I don't find anything about this problem on google, so could anyone give me some advice about it? I will be very appreciate.