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How To Run Muscle In Batch?

Hi everyone,

I am using muscle for multi-sequence alignment. My problem is I have several thousand input files, and need to run them in batch. 

    muscle3.8.31_i86linux64 -in a1.fa -out a1.afa
    muscle3.8.31_i86linux64 -in a2.fa -out a2.afa
    ...........
    muscle3.8.31_i86linux64 -in a3000.fa -out a3000.afa

Could anyone help me with a command to run them in batch? Thank you very much!

• 6,054 views • link
updated by Pierre Lindenbaum Pierre Lindenbaum • written by biolab biolab

1 answer

using GNU parallel:

ls *.fa | parallel  muscle3.8.31_i86linux64 -in {} -out {.}.afa

Using make with option -j (not tested):

%.afa:%.fa
    muscle3.8.31_i86linux64 -in $< -out $@

INPUT=$(shell ls *.fa)
.PHONY:all
all: $(patsubst %.fa,%.afa,${INPUT} )
• 310 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Thank you! It is really helpful.

• 0 views • link
written by biolab biolab

Further help needed: bash: parallel: command not found... Thanks a lot!

• 0 views • link
written by biolab biolab

I have sorted out the problem. Need to install GNU parallele. Thanks!

• 372 views • link
written by biolab biolab

Hi, I would like to run this but with mafft alingment. I searched in the parallel manual and several variations, I guess this is not an issue with the dot in the replacement string, I removed and it didn't work. The simple strategy is mafft seq.fa > align.fa so I tried ls *.fa | parallel linsi {} > ../{} to throw the results in a folder above. How could I fix this? Thanks

• 0 views • link
written by andrespara • andrespara

Hi, I would like to run this but with mafft alingment. I searched in the parallel manual and several variations, I guess this is not an issue with the dot in the replacement string, I removed and it didn't work. The simple strategy is mafft seq.fa > align.fa so I tried ls *.fa | parallel linsi {} > ../{} to throw the results in a folder above. How could I fix this? Thanks

• 0 views • link
written by andrespara • andrespara

Hi，I have a similar question about "ls *.fa | parallel linsi {} > ../{}". Have you solved it ?

• 0 views • link
written by 13657093870 • 13657093870

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