I am trying to use kraken to remove all contaminant reads/sequences from my Illumina data
So I am running kraken as described in the manual with the following script with input paired-end files R1_001.fastq R2_001.fastq
module load nixpkgs/16.09 intel/2016.4 kraken/1.1
module load jellyfish/1.1.11
kraken –threads 32 –db $
DBNAME –paired –check-names -out-fmt paired –fastq-output –unclassified-out M6_kra –output log.out R1_001.fastq R2_001.fastq
I am hoping to get M6_kra_R1.fq and M6_kra_R2.fq with no contaminant reads. Instead I get a file called M6_kra with only reads from R1_001.fastq.
Is there someway to output two fastq files?