I am trying to create synthetic reads from a fasta reference using BBMap's randomreads. Using this command from within the BBMap /sh directory:
[cmp07 sh]$ java -ea -Xmx23g -cp /home/mina/tools/BBMap-master/current/align2/RandomReads3.java ref=/home/mina/reference-genomes/N1a1.fasta reads=1258301 length=301 overwrite=f seed=-1 snprate=0.001 maxq=40 midq=30 minq=10 overlap=50
Unfortunately this produces and error:
Error: Could not find or load main class ref=.home.mina.reference-genomes.N1a1.fasta
How do I provide the path to my reference fasta file? Is there something I am missing about how to use this tool? Why are the slashes being converted to dots in the file path in the error message?