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.
Thank you.
Hi,
Regarding the error, you might consider to contact the author of the tool, Robert Edgar: https://www.drive5.com/muscle/. Although the tool is integrated in MEGA, so I'm not sure if the problem could be related with the implementation with that software too.
Did you try to use mafft: https://academic.oup.com/bib/article/20/4/1160/4106928
It has a dedicated server: https://mafft.cbrc.jp/alignment/server/large.html. Although I'm not sure if restricts the size or number of sequences that you can use in the alignment.
I hope this helps,
António
Hello and thank you so much for the response. I will be contacting MUSCLE, and that reminded me I should try to contact MEGA. Unfortunately, mafft doesn't work for what I'm doing as my sequences are too long.
Sorry to hear that.
Just curiosity: how many sequences are you trying to align? and how long they are?
About 500 sequences with around 55,000 nucleotides each, which explains the 30MB file.
I don't have experience on multiple sequence alignments, but I think that is very unlikely to do an MSA with this amount of sequences and length in a computer with only 8 Gb of RAM. I know that you mentioned the use of a computer with 100 (Gb? of RAM memory).
I used a long time ago the software Mega, but as far as I know this is a GUI program, not sure if you can run it in a cluster. Did you run Mega in your computer of 100 Gb of RAM memory? Is this a server?
When you run this in any of the computers, did you check the amount of RAM memory consumed before the tool break? Like with
htop?I'm thinking if this problem could be related with RAM memory, because you have a really big alignment.