Hi,
I'm sure this is really simple but can anyone tell me what is wrong in the following line:
spades.py --pe1-1 ./paired_end.1_trimmed.fq.gz --pe1-2 ./paired_end.2_trimmed.fq.gz \ --mp1-1 ./mate_paired.1_trimmed.fq.gz --mp1-2 ./mate_paired.2_trimmed.fq.gz \ -o ./mated_and_paired_ends
I keep getting the following error:
spades.py: error: Please specify option (e.g. -1, -2, -s, etc)) for the following paths: --mp1-1, ./mate_paired.1_trimmed.fq.gz, -o, ./mated_and_paired_ends
But I have already specified an option with --mp1-1?
Thanks!
As in
--mp-1 1 filename
and--mp-2 2 filename
. Not sure why you are still using--mp1-1
when command options are clearly telling you to use--mp-1
.