FORUMKraken ..not outputing two fastq files from paired-end reads
sjossey asked 5 months ago

  • Hi,
    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?

    1 Answers
    Best Answer
    Eloi Mercier Staff answered 5 months ago

  • Hi Sushma,
    this is a known bug in Kraken. This has been brought to the author’s attention but they haven’t replied yet. See
    Unfortunately, I do not know how to fix it right now.

    sjossey replied 5 months ago