segmentation fault muscle -align testing.fa -output alignment.afa

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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segmentation fault muscle -align testing.fa -output alignment.afa #76

Closed m-leitman closed 5 days ago

m-leitman commented 4 months ago

When I run the align command for two sequences, I get this error:

Input: 2 seqs, length avg 32604 max 33281

WARNING: Sequence length >5k may require excessive memory

00:00 12Mb 100.0% Derep 1 uniques, 0 dupes 00:00 14Mb 100.0% UCLUST 2 seqs EE<0.01, 1 centroids, 0 members 00:00 14Mb CPU has 8 cores, running 8 threads
zsh: segmentation fault muscle -super5 testing.fa -output alignment.afa

Does my device not have enough RAM to do this?

rcedgar commented 4 months ago

Yes, as the warning message says.

chingciripit commented 1 month ago

I am using muscle 3 and always get this error message. Tried it with only 17 protein sequences in fasta format

filtered_sequences_WP_only 17 seqs, max length 13477, avg length 2937 00:00:00 2 MB(0%) Iter 1 100.00% K-mer dist pass 1 00:00:00 2 MB(0%) Iter 1 100.00% K-mer dist pass 2 00:00:10 168 MB(1%) Iter 1 100.00% Align node 00:00:10 168 MB(1%) Iter 1 100.00% Root alignment 00:00:18 181 MB(1%) Iter 2 100.00% Refine tree 00:00:18 182 MB(1%) Iter 2 100.00% Root alignment 00:00:18 182 MB(1%) Iter 2 100.00% Root alignment zsh: segmentation fault muscle3 -in -out Refine biparts

Is it because the variation in the length of the protein sequences too large?

rcedgar commented 1 month ago

13477 is probably too long.