I have been trying to filter out low-quality bases on my task to conduct a variant annotation, meanwhile, I have completed all previous steps required. However, when I try to filter out low-quality bases after BQSR (GATK), the PathSeqFilterSpark did not yield a output file. There was no any ERRORS.

What I wrote was: gatk PathSeqFilterSpark --input output.bam

and once it did not work i wrote: gatk PathSeqFilterSpark --input output.bam --paired-output output_read_paired.bam

both did not yield either an output BAM file or an error