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multiscale / muscle3

The third major version of the MUltiScale Coupling Library and Environment
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Segmentation fault (core dumped) on FASTA file with 4 thousand sequences #278

Closed rhysf closed 7 months ago

rhysf commented 7 months ago

I am running MUSCLE v3.8.31 (compiled with GCCcore-9.3.0) on several FASTA files with 4,694 sequences in. I am running the following command:

muscle -in file.fa -out file.fa.muscle

Many of them worked, but about 1/3rd failed with an error:

Segmentation fault (core dumped)

and results in a large core file.

Normally, I would simply increase RAM, but in this case, I am certain that I have higher RAM than appears to be in use based on the warnings. Specifically, I've given 16Gb RAM for one such alignment and had the following warnings:

KOG0188 4694 seqs, max length 2868, avg length 979 00:02:03 222 MB(-11%) Iter 1 100.00% K-mer dist pass 1 00:02:04 222 MB(-11%) Iter 1 100.00% K-mer dist pass 2 00:06:04 3842 MB(-187%) Iter 1 100.00% Align node
00:06:05 3852 MB(-188%) Iter 1 100.00% Root alignment 00:32:42 3854 MB(-188%) Iter 2 100.00% Refine tree
00:32:43 3854 MB(-188%) Iter 2 100.00% Root alignment 00:32:44 3854 MB(-188%) Iter 2 100.00% Root alignment Segmentation fault (core dumped)

I have also tried with much higher RAM, but still got the same issue?

Are there any suggestions of what else might be causing this issue?

Thanks, Rhys

LourensVeen commented 7 months ago

Hi Rhys,

I would love to help you, but I'm afraid there's been a mixup: This is the GitHub repository for the MUltiScale Coupling Library and Environment (MUSCLE), while you're using MUltiple Sequence Comparison by Log-Expectation (MUSCLE). It seems the sequence alignment tool actually predates the model coupling framework by a year or two, but I guess the people who named the latter didn't know about the former, and now we're all confused.

I have a rough idea of what sequence alignment is, and log-expectations are always a good idea, but I don't know anything about the software. Google suggests you may be able to get help at https://drive5.com/muscle/manual/support.html

rhysf commented 7 months ago

apologies for the mix up. Thanks.