Spades output help

Question

[niyomiw88]

Every time I try to run this on command line it gives me an error saying that output directory is not specified. What else should i include to specify the output directory?

spades.py -k 73,75,77 --careful --only-assembler -s <Pediculus-humanus-USDA_CONTIGS_PhumU2.fa> -o test1

Answer 1

[JC]

If that is your exact command, the "<" and ">" means something different to the shell (I/O redirection), I think you need:

spades.py -k 73,75,77 --careful --only-assembler -s pediculus-humanus-usda_contigs_phumu2.fa -o test1

[niyomiw88]

Thank you so much! It actually worked :D