Adapter Trimming on PE reads have different number of reads output

[bshim181]

Hello,

trim_galore -o output --fastqc --paired $R1_file $R2_file

I have utilized trim-galore to trim illumina adapters on my PE sequencing reads. When I tried to process the output fq files through bbmerge for insert length analysis, I have received this error message from bbmerge. "There appear to be different numbers of reads in the paired input files. The pairing may have been corrupted by an upstream process."

So when I checked the length of trim-galore outputs for one of the samples, output from R1 and R2 differed. Would I have to specify retained_unpaired for these to match up? My assumption was that if I run trim-galore with paired parameters, the pairings would be retained.

314343816 Sample1_R1_001_val_1.fq 299531972 Sample1_R2_001_val_2.fq