tag 18218 notabug thanks On 08/07/2014 03:29 PM, YANG LIU wrote: > Hello, > > I intend to convert some files to the space-separated format and thus input > the following command in the Terminal using Ubuntu, > > Nico@frs3623:~/Documents/Control$ *grep -d ">" SRR21807.fasta | sort | uniq > -c > SRR21807.txt*
Your description is a bit confusing - your sample command appears to be searching for ">", not spaces, so I don't know what "space-separated format" has to do with your actual problem. > > Unfortunately, the returning message is, > > grep: invalid argument ‘>’ for ‘--directories’ That's because you did the same as if you had typed: grep --directories=">" SRR21807.fasta ... The short option -d requires an option (one of 'read', 'recurse', or 'skip'), the same as its long option counterpart --directories. Note that --directories=recurse has a shorthand of -r. Are you trying to use SRR21807.fasta as a directory name and recurse through all files underneath it? If so, use: grep -r ">" SRR21807.fasta or grep -d recurse ">" SRR21807.fasta Or is SRR21807.fasta a regular file? If so, use: grep ">" SRR21807.fasta > Could you figure out what incurred this error and how to fix it via > modifying my command? I appreciate your help. I don't know enough about your setup to know what you wanted to do, but it should be fairly obvious from the error message that your problem was invalid usage on your part, and not a bug in grep. Feel free to ask more questions or give us more details about your situation, but at this point, I'm closing this bug so that it doesn't show up as an unresolved issue in grep in our bug tracker. -- Eric Blake eblake redhat com +1-919-301-3266 Libvirt virtualization library http://libvirt.org
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