Trouble running Muscle on Mac OS

Question

[ricfoz]

Hello community,

I am trying to align a base with 22 sequences of a max length of 483656 base pairs, it is long, but not very, i am using a Sierra Mac OS, and i am using Muscle v3.8.31. I have used the following command line while standing where the program muscle is and where the base to be aligned is also saved, in order to do the alignment as suggested by the program tutorial:

Path/to/muscle -in File.to.align.fasta -out Output.file.name.afa -maxiters 1 -diags

and after days of running i got the next output:

File.to.align. 22 seqs, max length 483652, avg length 253004 00:00:02 35 MB(0%) Iter 1 100.00% K-mer dist pass 1 00:00:02 35 MB(0%) Iter 1 100.00% K-mer dist pass 2 Killed: 9 928 MB(11%) Iter 1 100.00% Align node

It strikes me that all three processes have a 100% advance, but the last one says "Killed", the number in brackets is 11%, and it gives no output, i guess the output should have been saved in the same folder, but it was not created.

Anyone has any idea what could have happened?, or where could the output be if it actually finished?

Answer 1

[Michael]

Hi, I have the impression that this might be a memory problem. Macs often don't have what it takes in RAM (>=128G) to run large compute jobs. Your options are either to try other programs like MAFFT, clustalO, T-coffe, etc. or get a high RAM node. If you could post your input file, I or someone else could give it a try on a Linux node.

[ricfoz]

Michael Donrup

Thanks a lot for your answer, i have been reading about MAFFT and the other programs you suggest, i will give them a try. I am working with a dataset which i am not allowed to share plus, i am stubborn enough to try to get the job done with the resources i've got. Still, i am grateful for your offer, and will for sure let you know which MSA program did the job !

Best regards

[ricfoz]

Beauty of beauties, i have run my work with MAFFT, as you suggested. It ran neatly and fast. Thanks a lot for the suggestion of programs, and for everyone who run with this trouble, or question, i leave a paper that helped me, just as smoothly as Michael Dondrup's post:

Sviatopolk-Mirsky Pais, de Cassia Ruy, Oliveira, Santos Coimbra, (2014); Assessing the efficiency of multiple sequence alignment programs. Algorithms for Molecular Biology, 9:4

Thanks and best regards

ricfoz.