Paired input to kneaddata resulting in unpaired files

When running kneaddata, my paired input is ending up as entirely unpaired. I have tried adding “/1” and “/2” as a suffix to the read headers, but the kneaddata_paired.fastq output files are blank while kneaddata_unpaired.fastq contain all the reads.

It appears that trimmomatic is doing just fine with tracking R1/R2 pairs, but sometime after that step the pairs get lost.

My files are named Sample1.R1.fastq.gz and Sample1.R2.fastq.gz

An example of my R1 and R2 file headers:


Here is my kneaddata command:

kneaddata --input1 Sample1.R1.fastq.gz --input2 Sample1.R2.fastq.gz -db /pathtodb/kneaddata_db --output Sample1_kneaddata_output

Here is a count of reads in all the output files created:

R1 R2
Input Reads 85,362,781 85,362,781
Sample1_bowtie2_paired_contam.fastq - -
Sample1_bowtie2_unmatched.fastq 23,682 6,117
Sample1_kneaddata_paired.fastq - -
Sample1_kneaddata.repeats.removed.fastq 80,698,325 80,698,490
Sample1_kneaddata.repeats.removed.unmatched.fastq 1,909,623 1,291,362
Sample1_kneaddata.trimmed.fastq 81,153,744 81,153,744
Sample1_kneaddata.trimmed.single.fastq 1,921,519 1,299,530
Sample1_kneaddata_unmatched.fastq 82,584,266 81,983,735

And version info:

kneaddata v0.12.0

Any help would be greatly appreciated! It’s ok if this is just a bug with kneaddata because I just plan on concatenating the R1/R2 reads to use in Humann analysis, but I do want to make sure that something isn’t going wrong with my analysis before I move onto the next step.