fastqcSplitDups.py only outputs files for R1 when -r2 is also used

[HeatherKates]

Hello, my run command is:
python mcscript/fastqSplitDups.py -r1 RAPiD-Genomics_FMN_131001_P001_WA03_R1.concat.fastq -r2 RAPiD-Genomics_FMN_131001_P001_WA03_R2.concat.fastq --outdir deduplicate/ --out summary.csv --debug

The log output is:

2018-07-12 11:23:09,088 - INFO - Starting mcscript/fastqSplitDups.py
2018-07-12 11:23:09,089 - INFO - Running script from /ufrc/soltis/hkates/NITFIX/Atram_Deduplication_Tests/mcscript
2018-07-12 11:23:09,089 - INFO - Git commit id: c6aef49
2018-07-12 11:23:09,089 - INFO - Reading 'RAPiD-Genomics_FMN_131001_P001_WA03_R1.concat.fastq'
2018-07-12 11:23:09,253 - INFO - Finished reading 'RAPiD-Genomics_FMN_131001_P001_WA03_R1.concat.fastq'
2018-07-12 11:23:09,253 - INFO - Reading 'RAPiD-Genomics_FMN_131001_P001_WA03_R2.concat.fastq'
2018-07-12 11:23:09,403 - INFO - Finished reading 'RAPiD-Genomics_FMN_131001_P001_WA03_R2.concat.fastq'
2018-07-12 11:23:09,951 - INFO - Script complete.

But output files (e.g. *distinct *duplicate *uniq) are only generated for the R1 sample.

Thank you for any input!