I am having a issue trying to run a local rpsblast on all the files in a specified directory. I believe it's a syntax issue. Here's what I have below.
system'rpsblast -i NC_017249.faa –d PFAM2/pfam -o file.out';
I have tried it with and out the 's, with "s and (). Still no luck, But if I copy/paste just the command into a command prompt it works no problem. Here is the error message below
rpsblast 2.2.24 ERROR: Arguments must start with '-' (the offending argument #3 was: 'ûd')

In reply to Running rpsblast on all files in directory, using perl by MoniqueLT

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