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Bash on CygWin

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I am using CygWin to run a bash file but I am getting weird results.

Code:

#!/bin/bash
mkdir CLEANDATA
mv *FASTA CLEANDATA
cd CLEANDATA
ls
echo "COMPLETE"

And this is what I get
Code:

$ ./Pipe.txt
./Pipe.txt: line 5: $'ls\r': command not found
COMPLETE

Moreover, the new folder is named CLEANDATA* instead of CLEANDATA.
Any help will be very much appreciated

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