When trying to filter reads using bbduk, I get the following error message:
maskMiddle was disabled because useShortKmers=true
Exception in thread "main" java.lang.RuntimeException: Can't read file '/home/bioinf/TrainingData/SRR6197336/SRR6197336_1.fastq'
This is my code:
~/Downloads/bbmap/bbduk.sh in1=~/TrainingData/SRR6197336/SRR6197336_1.fastq in2=~/TrainingData/SRR6197336/SRR6197336_2.fastq out1=~/TrainingData/reads/bbduk/SRR6197336_1_bbduk.fastq out2=~/TrainingData/reads/bbduk/SRR6197336_2_bbduk.fastq ktrim=r k=23 mink=11
I am not really sure what is going wrong here. Any help would be appreciated!