Empty VCF file after runnin gHaplotypeCaller

Hi GATK team,

I'm running HaplotypeCaller using the following command:

-T HaplotypeCaller -R all.chrs.fasta -I filename.bam -o filename.vcf -stand_emit_conf 10 -stand_call_conf 20 -nct 8 -rf BadCigar

on PacBio reads aligned to a reference genome using BWA.

I don't know why I'm getting an empty VCF file. Please find attached the log file. I see that ~50% of the reads are filtered out but the second half should produce some variants, shouldn't it? Is it a coverage issue now?

Appreciate a lot you help and thanks in advance for any piece of advice!