Filtered reads not written to file

[donovan-h-parks]

Hi. I'm running fastp on PE data with the --out1, --out2, --unpaired1, --unpaired2, and --failed_out flags. fastp reports that reads failed due to too short: 32 and indeed if I check the output files I am missing 16 forward and 16 reverse reads. However, the failed and unpaired output files are all empty. I was expecting to see these 32 reads in one of these files.

Should all reads be accounted for or is there a situation where a read is not ultimately written to any of the output files?

[sfchen]

What's your fastp version?

[donovan-h-parks]

fastp 0.23.1

If it helps, I have verified that the 16 filtered forward and reverse reads are due to adapter trimming.

[donovan-h-parks]

Command: fastp --in1 reads_R1.fq.gz --in2 reads_R2.fq.gz -u 30 -l 70 --cut_mean_quality 15 --cut_front --cut_front_window_size 1 --cut_tail --cut_tail_window_size 1 --cut_right --cut_right_window_size 4 --trim_poly_x --poly_x_min_len 12 --detect_adapter_for_pe --out1 reads_R1.qc.fq.gz --out2 reads_R2.qc.fq.gz --unpaired1 singletons.qc.fq.gz --unpaired2 singletons.qc.fq.gz --failed_out failed.qc.fq.gz --json fastp/read_qc/fastp.json --html fastp/read_qc/fastp.html --thread 4