I have a very large .FASTA file 30MB that I am trying to MUSCLE align on MEGA X (mac) but after around 8 hours I'll get the error message "Error-Alignment Failed: MUSCLE Log file did not end properly".
My computer only has 8GB of memory so I tried the same file on a computer with around 100 and got the same error. I am only doing 1 iteration and I increased the max MB all the way up. This error always shows up at the root alignment stage. I tried splitting up the FASTA file into 12 files and it actually worked, however when I tried to recombine and re-align them I got the same error message.
Is there another software I should be using for such a large file? I can't find anything online about what this error message means and how to fix it.