parallel program for running a command for several files
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6.2 years ago

Hi I have a command to run a module in software Homer the command is the following

findMotifsGenome.pl ERCreInput mm10 motifs/instance/  -find motifs/motif1.motif > motifs/instance/motif1.motif.txt


I want to run the above command using parallel program for several files that are contained in folder motifs/. The files are starting with names motif1.motif and so on. I want to output the files in motifs/instance/motif1.motif.txt. I tried out the following

parallel 'findMotifsGenome.pl ERCreInput mm10 motifs/instance/ -find motifs/{} > motifs/instance/{.}.txt' ::: *.motif


Somehow it is not working can anyone please give me suggestion how correct the code so that it works

parallel Forum • 2.2k views
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Does it throw an error message or just fails? make sure you use parallel correctly, there are several versions with different usage

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Type parallel --version and check that you are using GNU parallel by Ole Tange. You should get something like this:

\$ parallel --version
GNU parallel 20160422
Ole Tange and Free Software Foundation, Inc.
This is free software: you are free to change and redistribute it.
GNU parallel comes with no warranty.

Web site: http://www.gnu.org/software/parallel

When using programs that use GNU Parallel to process data for publication
please cite as described in 'parallel --citation'.


Otherwise you are using the bash parallel command from moreutils, which has a different syntax.

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So in my case i getting the following error Reading input files... 11466 total sequences read !!! Couldn't open motif file: motifs/*.motif !!! Finding instances of 0 motif(s) so somehow the motifs file are not detected using the above command

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Can you type the following:

parallel --version

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GNU parallel 20160422 Copyright (C) 2007,2008,2009,2010,2011,2012,2013,2014,2015,2016 Ole Tange and Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html This is free software: you are free to change and redistribute it. GNU parallel comes with no warranty.

Web site: http://www.gnu.org/software/parallel

When using programs that use GNU Parallel to process data for publication please cite as described in 'parallel --citation'.

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Entering edit mode

So in my case i am getting the following error Reading input files... 11466 total sequences read !!! Couldn't open motif file: motifs/*.motif !!! Finding instances of 0 motif(s) so somehow the motifs file are not detected using the above command

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Entering edit mode

It looks like you are not in the correct folder? Parallel is replacing {} with *.motif because there aren't any files in your current folder that matches *.motif.