Segmentation fault (core dumped) error in MUSCLE
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4 weeks ago

I am trying to analyse some NGS data and have come to a stand still. I have very little bioinformatics experience so any guidance would be fantastic.

The fasta files I'm working with consist of ~370,000 reads (viral genome) with an average length of 150bp. When I try to align the files using MUSCLE in terminal I get the following error 'Segmentation fault (core dumped)'. Is this because my computer isn't powerful enough to process these files?

I have 32gb of RAM, 8 thread 4 core CPU, Nvidia 2060 GPU..

NGS alignment fastq linux sequence • 189 views
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4 weeks ago

MUSCLE is a multiple sequence alignment program, now this might sound a bit confusing but this doesn't mean it is meant to align very many sequences (especially not that many), at least not to a single reference. It tries to align all sequences (maybe max a few hundred) with each other to discover a consensus, which is not what you want to do with short sequencing reads. You should instead use a short read aligner, like bwa, hisat, or bbmap, see a list here. In fact what your computer is likely telling you is that you are running out of memory because you are using the wrong tool.

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Thank you so much!


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