Hi everyone, 

I am using bio3d package for some sequence analysis because of its nice integrated MUSCLE execution. However, I have been encountering some errors while I was running seqaln function, which calls for installed MUSCLE program. In my case, I stored the MUSCLE program on the desktop with pathway of "./Desktop/muscle/src/muscle". I had no problem running MUSCLE directly from terminal. However, when I'm calling the exepath in R, it keeps giving me error messages. Below are some errors I have encountered. Your help will be much appreciated. 

> aa<-read.fasta("./R/test.fa", rm.dup=F)

> aln<-seqaln(aa, exepath="/Users/Fan/Desktop/muscle/src/muscle", file="aa_muscle.fa", protein=T) 
/Users/Fan/Desktop/muscle/src/musclemuscle -in /var/folders/v9/v95dzKP2E9SAkmd7m4T8dE+++TQ/-Tmp-//RtmpKUJVlZ/file618fb492 -out aa_muscle.fa  -stable -seqtype protein/bin/sh: /Users/Fan/Desktop/muscle/src/musclemuscle: No such file or directory 
Error in file(file, "r") : cannot open the connection 
In addition: Warning message: 
In file(file, "r") : 
  cannot open file 'aa_muscle.fa': No such file or directory  
 
I have also noticed that the example file from bio3d/seqaln does not have quotation marks for the exepath. But it returned a different error message.

> aln<-seqaln(aa, exepath=/Users/Fan/Desktop/muscle/src/muscle, file="aa_muscle.fa", protein=T) 
Error: unexpected '/' in "aln<-seqaln(aa, exepath=/" 
or > aln<-seqaln(aa, exepath=Users/Fan/Desktop/muscle/src/muscle, file="aa_muscle.fa", protein=T) 
Error in paste(exepath, "muscle -in ", toaln, " -out ", file, " ", extra.args,  :  
  object 'Users' not found

Thank you for your help ahead of time! 

Best wishes.

Fan
  
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