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It wasn't recognizing the -i because it was a long "-" not a short one. Must have been from copying from word into the command line. WOW!
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This is a pretty common problem on both PC/mac OS. You should turn off "smart" hyphens (and other smart things) in keyboard preferences. -
Nice work j.cappellazzi!
I hadn't heard of that hyphen issue - bit of a trap!
The "./" in my command refers to a 'relative' path. I.e., it will look for a folder that is in your current directory. This is in contrast to absolute paths, i.e., "/home/qiime/Desktop/Hilo_New/" that will work no matter where you run them from.
I think the problem with my original command is that the folder name and the name in the command were slightly different. You created a folder called "FastX-filterFastq", but the command is trying to create output here "./fastX-filterFastq/". Note the lower-case 'f' in fastX.
Anyway, glad you got it working!
Cheers,
Matt.Comment
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