Question: problem with MUSCLE
0
gravatar for alec_djinn
4 months ago by
alec_djinn320
European Union
alec_djinn320 wrote:

I am using MUSCLE v3.8.1551 to align some DNA sequences. I am not sure why, but I am getting over and over the same error (I have never had this error before):

18896 bus error

Here an example of the output I get.

$ muscle -in ./BmEyKvwTAOdeDVtb_split.tmp -out ./BmEyKvwTAOdeDVtb_msa.tmp

MUSCLE v3.8.1551 by Robert C. Edgar

http://www.drive5.com/muscle
This software is donated to the public domain.
Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97.

BmEyKvwTAOdeDVtb_split 38 seqs, lengths min 4966, max 10900, avg 10652
00:00:01      3 MB(0%)  Iter   1  100.00%  K-mer dist pass 1
00:00:01      3 MB(0%)  Iter   1  100.00%  K-mer dist pass 2
00:02:24   957 MB(11%)  Iter   1  100.00%  Align node       
00:02:24   958 MB(11%)  Iter   1  100.00%  Root alignment
00:04:49   987 MB(11%)  Iter   2  100.00%  Refine tree   
00:04:49   987 MB(11%)  Iter   2  100.00%  Root alignment
00:04:49   987 MB(11%)  Iter   2  100.00%  Root alignment
[1]    18896 bus error  muscle -in ./BmEyKvwTAOdeDVtb_split.tmp -out ./BmEyKvwTAOdeDVtb_msa.tmp

As you can see the algorithm works until almost the end, then it crashes. The files .tmp are in fasta format. I don't know what to do about it, I have tried to reinstall MUSCLE but it did not solve. I am not even sure if it is a MUSCLE problem. Can someone point me to a possible solution?

dna muscle alignment • 178 views
ADD COMMENTlink written 4 months ago by alec_djinn320

See https://stackoverflow.com/questions/212466/what-is-a-bus-error How much memory do you have on this machine?

ADD REPLYlink modified 4 months ago • written 4 months ago by genomax34k

16GB, I don't think the memory is the problem, I am monitoring it and MUSCLE is not using much of it.

ADD REPLYlink modified 4 months ago • written 4 months ago by alec_djinn320
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