gatk error...

gatk error https://gatkforums.broadinstitute.org/gatk/discussion/24492/mutect2-java-lang-illegalargumentexception-cannot-construct-fragment-from-more-than-two-reads#latest

variants/somatic_vc.sh

@@ -115,7 +115,7 @@ then
   gatk4_dbsnp=${index_path}/clinseq_prj/dbSnp.gatk4.vcf.gz
   module load gatk/4.1.4.0 picard/2.10.3 snpeff/4.3q samtools/gcc/1.8 vcftools/0.1.14
   java -XX:ParallelGCThreads=$NPROC -Djava.io.tmpdir=./ -Xmx16g  -jar $PICARD/picard.jar CollectSequencingArtifactMetrics I=${tumor} O=artifact_metrics.txt R=${reffa}
-  gatk --java-options "-Xmx20g" Mutect2 $ponopt -R ${reffa} -I ${tumor} -tumor ${tid} -I ${normal} -normal ${nid} --output ${tid}.mutect.vcf
+  gatk --java-options "-Xmx20g" Mutect2 $ponopt  --independent-mates -RF AllowAllReadsReadFilter -R ${reffa} -I ${tumor} -tumor ${tid} -I ${normal} -normal ${nid} --output ${tid}.mutect.vcf
   gatk --java-options "-Xmx20g" FilterMutectCalls -R ${reffa} -V ${tid}.mutect.vcf -O ${tid}.mutect.filt.vcf
   vcf-sort ${tid}.mutect.filt.vcf | vcf-annotate -n --fill-type | java -jar $SNPEFF_HOME/SnpSift.jar filter -p '(GEN[*].DP >= 10)' | bgzip > ${pair_id}.mutect.vcf.gz
 elif [ $algo == 'varscan' ]