Question: Problem in in alignment by muscle
0
gravatar for misbahabas
2.0 years ago by
misbahabas60
misbahabas60 wrote:

Hello

I want to perform multiple sequence alignment by muscle but after running it abort or kill the process, input file contain gene sequence of 29 species in fasta format

/usr/bin/muscle -in AMY2B_ALIGNED.fa -out tset_output.fa

after some time it give error

zsh: abort /usr/bin/muscle -in AMY2B_ALIGNED.fa -out tset_output.fa

and no output file generated . Please give me any idea about it

thankx in advance

muscle tool sequence alignment • 1.7k views
ADD COMMENTlink modified 2.0 years ago by natasha.sernova3.5k • written 2.0 years ago by misbahabas60

I am not quite sure, but muscle may have some limits for input file size. What size does your input file have?

What species do you work with? In case of eukaryotes, your input may be quite large. Do you work with nucleotides or proteins? Muscle deals with both, and you didn't tell anything about.

Try this run with just two entries.

seq1

artfh

seq2

asrtg

What is the result?

Muscle does not complain it didn't find you input. But to be on the safe side check its location.

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by natasha.sernova3.5k

I am working on all vertebrates and file which is running is 771.1KB, and working on nucleotides

the result of above seq is muscle -in test1.fa -out out1.fa output

seq1

ARTFH

seq2

ASRTG

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by misbahabas60

then is used muscle for 32 bit and some changing

use this command

muscle3.8.31_i86linux32 -in AMY2B_ALIGNED.fa -out aligned_output.fa -verbose -maxiters 1

it give error like this

OUT OF MEMORY **

Memory allocated so far 4284.6 MB

No alignment generated**

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by misbahabas60

OUT OF MEMORY

The error is clear. Muscle ran out of memory. If you are using 32-bit Muscle then you should change to 64-bit Muscle and a machine with more RAM.

ADD REPLYlink written 2.0 years ago by genomax70k

So muscle is a problem. Try MAFFT, for example: http://mafft.cbrc.jp/alignment/software/

I'm not sure but it may be more generous in terms of memory usage. It is.

For 64bit x86

mafft-7.271-gcc_fc6.x86_64.rpm (built on kernel 2.6)

This version uses at most x2 memory space in comparison with previous versions.

If it stops due to memory shortage, try version 7.222

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by natasha.sernova3.5k

when i use 64bit It give above error like

zsh: abort /usr/bin/muscle -in AMY2B_ALIGNED.fa -out tset_output.fa

and machine RAM is 8GB

ADD REPLYlink written 2.0 years ago by misbahabas60

Do you still have problems? There are more different tools here.

http://www.ebi.ac.uk/Tools/msa/

I found it in this post which one is good mafft or clustalW???

ADD REPLYlink modified 24 months ago • written 24 months ago by natasha.sernova3.5k
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