I have run kneaddata 0.12.0 on my metagenomics data. The data do not need to removed host-genome-contaminated reads, thus only use the trimmomatic options.
kneaddata
-i1 sample_1.fq.gz
-i2 sample_2.fq.gz
-o kneaddata -v -t 64
–remove-intermediate-output
–trimmomatic $PATH/soft/Trimmomatic-0.39/Trimmomatic-0.39/
–trimmomatic-options ‘LEADING:20 TRAILING:20 SLIDINGWINDOW:5:20 AVGQUAL:20 MINLEN:50’
I have *_1_kneaddata.trimmed.1.fastq and *_1_kneaddata.trimmed.2.fastq for each sample. But the title of reads do not put the paired-end symble “1” and “2” behind “#”, as the figure below.
Then when I used metawrap binning, a wrong message was report as the below figure.
But when I used kneaddata v0.7.6 with the same code, the result is correct,the paired number 1 and 2 was behind #.
How can I go about pairing these read correctly?
Thanks!