FastQC and Trimmomatic in Galaxy?

I am independently working on data retrieved SRA database, paired-end data as separate inputs. After running FastQC using Galaxy, majority of the modules have failed. I tried Trimmomatic with default settings (Avg quality =20, number of bases to avg across = 4), it resulted in R1 and R2 paired and unpaired (4 total outputs). I ran FastQC again, which rendered some changes (per base sequence quality passed) but resulted in other modules (Sequence length distribution and per tile quality scores) getting a warning sign or failing. IS there specific setting other than default that provides better results? What output should i use from Trimmomatic for fastqc again?