Problem in in alignment by muscle
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
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misbahabas •
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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.
artfh
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.
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
ARTFH
ASRTG
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**
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.
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
If it stops due to memory shortage, try version 7.222
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
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???