The bioBakery help forum

Interpreting file names and sizes

I ran kneaddata using a reference database. It appears that the reference I used is either not in the reads or was a poor choice for removing host. In either case, I’m a bit confused by the output. Can you tell me from where the concatenated fastq file is derived? I thought it was the final paired_[12].fastq. However, it must be coming from something else as my final paired has zero data but the concatenated fastq has reads. I’ve bolded (assuming I formatted things correctly) the files to which I refer, but kept the whole lot of 'em in there so that you have context.

FileSize	Name
0	17M-Spleen-CL-2021_CanFam3.1_bowtie2_paired_contam_1.fastq
0	17M-Spleen-CL-2021_CanFam3.1_bowtie2_paired_contam_2.fastq
724135591	17M-Spleen-CL-2021_CanFam3.1_bowtie2_unmatched_1_contam.fastq
672468730	17M-Spleen-CL-2021_CanFam3.1_bowtie2_unmatched_2_contam.fastq
**121035977	17M-Spleen-CL-2021.fastq**
26735	17M-Spleen-CL-2021.log
**0	17M-Spleen-CL-2021_paired_1.fastq**
**0	17M-Spleen-CL-2021_paired_2.fastq**
738898305	17M-Spleen-CL-2021.repeats.removed.1.fastq
683896647	17M-Spleen-CL-2021.repeats.removed.2.fastq
49595847	17M-Spleen-CL-2021.repeats.removed.unmatched.1.fastq
45249499	17M-Spleen-CL-2021.repeats.removed.unmatched.2.fastq
835919144	17M-Spleen-CL-2021.trimmed.1.fastq
765942592	17M-Spleen-CL-2021.trimmed.2.fastq
61455491	17M-Spleen-CL-2021.trimmed.single.1.fastq
51413620	17M-Spleen-CL-2021.trimmed.single.2.fastq
64358561	17M-Spleen-CL-2021_unmatched_1.fastq
56677416	17M-Spleen-CL-2021_unmatched_2.fastq