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rcedgar / muscle

Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted structures.
https://drive5.com/muscle
GNU General Public License v3.0
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Fatal error mpcflat.cpp assert failed #11

Closed jianshu93 closed 2 years ago

jianshu93 commented 2 years ago

muscle 5.0.1428_linux64 791Gb RAM, 24 cores (C) Copyright 2004-2021 Robert C. Edgar. https://drive5.com

Hello Robert,

I have the following error when running muscle. There supper5 one is good.

muscle -align ASVs1.fa -output aln.afa -threads 24 Elapsed time 01:27:16 Max memory 0.0b

---Fatal error--- mpcflat.cpp(170) assert failed: PairCount == PairCount2 5140.18user 87.93system 1:27:24elapsed 99%CPU (0avgtext+0avgdata 194959560maxresident)k 62000inputs+24outputs (11major+41593028minor)pagefaults 0swaps

Thanks,

Jianshu

rcedgar commented 2 years ago

If you can post ASVs1.fa, happy to take a look. However, I'm going to bet ASVs are 16S or ITS, in which case making an MSA is probably a bad idea, these genes are much too diverse in a typical sample. Why are you aligning them?

rcedgar commented 2 years ago

Closed due to no response.