Problem in in alignment by muscle

Question

[misbahabas]

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

Thanks in advance

[natasha.sernova]

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.

[misbahabas]

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

[misbahabas]

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**

[GenoMax]

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.

[natasha.sernova]

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

[misbahabas]

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

[natasha.sernova]

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???