I am trying to perform an alignment of 11 very long (whole chromosome) DNA sequences using Muscle 3.8.31 for Linux, but am encountering a problem.
This is my input:
muscle-3.8.1 -diags -in S_ratti_Chr2.fa -out S_ratti_Chr2.afa
The code seems to run for a while, but then I get the following:
S_ratti_Chr2 11 seqs, max length 16759905, avg length 16759518 00:48:36 1053 MB(65%) Iter 1 1.52% K-mer dist pass 1 00:48:47 1053 MB(65%) Iter 1 100.00% K-mer dist pass 1 00:48:47 1053 MB(65%) Iter 1 1.52% K-mer dist pass 2 00:48:47 1053 MB(65%) Iter 1 100.00% K-mer dist pass 2 00:49:07 24533 MB(100%) Iter 1 10.00% Align node /cm/local/apps/torque/220.127.116.11/spool/mom_priv/jobs/4974615.master.cm.cluster.SC: line 15: 95045 Killed muscle-3.8.1 -diags -in S_ratti_Chr2.fa -out S_ratti_Chr2_2.afa
No output file is generated. I am very new to bioinformatics and this is the first time I have attempted to use Muscle (or any aligning method); could anyone help me understand why the command is failing? Lay terminology would be greatly appreciated as I am also not very familiar with coding. I'd also like to hear of any other aligning methods if there are any generally considered better than Muscle.
Many thanks in advance.