I installed Longstitch and ran the test script with no issues. The output files matched the expected output files. But when I am now trying to run Longstitch on my own data I am getting this error.
(medaka) operations@LabPC1:~/medaka/longstitch-1.0.5$ ./longstitch run draft=~/medaka/~medaka/medaka_results/consensus.fa reads=~/medaka/combined.fastq G=4.5e8
make: command: Command not found
make: command: Command not found
make: *** No rule to make target '/home/operations/medaka/~medaka/medaka_results/consensus.fa.fa', needed by '/home/operations/medaka/~medaka/medaka_results/consensus.fa.cut250.tigmint.fa'. Stop.
I changed the file name from .fasta to .fa for my draft assembly because it requires a .fa file, but now I am getting ".fa.fa" What is wrong here?