Kneaddata errors and output files

As someone who is quite new to this, I’m having several difficulties that might have a really simple solution

  1. Trimmomatic issue
  • since I’ve been getting errors whenever I try to just use [kneaddata --trimmomatic], I bypass this problem by listing out the path, but now I can’t add options to trimmomtatic [kneaddata --trimmomatic /home/aaa/bbbb/trimmomatic-0.39-2 -options "SLIDINGWINDOW:15:20]. I get “unrecognized arguments: SLIDINGWINDOW:15:20”. Same error message shows up even when I removed quotation mark. How do I add options after specifying path
  1. Output Files
  • the command I used is this [kneaddata --input1 25_CT037_1.fastq --input2 25_CT037_2.fastq --reference-db /home/sam/database/hg37dec_v0.1.4.bt2 --trimmomatic /home/sam/anaconda3/share/trimmomatic-0.39-2 --output work]. My output files are “25_CT037_1_kneaddata_hg37dec_v0.1_bowtie2_paired_contam_1.fastq”, “25_CT037_1_kneaddata_hg37dec_v0.1_bowtie2_paired_contam_2.fastq”, “25_CT037_1_kneaddata_hg37dec_v0.1_bowtie2_unmatched_1_contam.fastq”, “25_CT037_1_kneaddata_hg37dec_v0.1_bowtie2_unmatched_2_contam.fastq”,
    “25_CT037_1_kneaddata_unmatched_1.fastq”, and
  • Could be a silly question but what happened to 25_CT037_2?
  • I saw some of the guides showing output file with the word “repeat” on the file name. Is that some other option I should add?

So to answer my own question after asking around and just trying it.
Trimmomatic issue is simple, probably someone with even a little experience using bio tools will know how to resolve the issue. Basically write trimmomatic twice. trimmomatic /PATH trimmomatic-option

Output file numbers will depend if you choose to delete intermediate files. I was deleting intermediate files so didn’t get all the files. But, in the end I think you are only expected to use paired output files.