error: list index out of range

[xhuashen]

Dear developers,
when I run EnsembleTR to merge TR calls from different TRcallers, I encounter a error like
Traceback (most recent call last):
File "/qitinglab/shenlongxin/cache/conda/envs/EnsembleTR/bin/EnsembleTR", line 8, in
sys.exit(run())
File "/qitinglab/shenlongxin/cache/conda/envs/EnsembleTR/lib/python3.8/site-packages/ensembletr/main.py", line 80, in run
retcode = main(args)
File "/qitinglab/shenlongxin/cache/conda/envs/EnsembleTR/lib/python3.8/site-packages/ensembletr/main.py", line 46, in main
recresolver = recordcluster.RecordResolver(rc)
File "/qitinglab/shenlongxin/cache/conda/envs/EnsembleTR/lib/python3.8/site-packages/ensembletr/recordcluster.py", line 528, in init
self.rc_graph = ClusterGraph(rc)
File "/qitinglab/shenlongxin/cache/conda/envs/EnsembleTR/lib/python3.8/site-packages/ensembletr/recordcluster.py", line 440, in init
self.graph = self.BuildGraph()
File "/qitinglab/shenlongxin/cache/conda/envs/EnsembleTR/lib/python3.8/site-packages/ensembletr/recordcluster.py", line 454, in BuildGraph
allele_list = self.GetAlleleList()
File "/qitinglab/shenlongxin/cache/conda/envs/EnsembleTR/lib/python3.8/site-packages/ensembletr/recordcluster.py", line 482, in GetAlleleList
allele = Allele(ro, al_idx)
File "/qitinglab/shenlongxin/cache/conda/envs/EnsembleTR/lib/python3.8/site-packages/ensembletr/recordcluster.py", line 330, in init
self.allele_sequence = ro.prepend_seq + alleles[al_idx] + ro.append_seq
IndexError: list index out of range
my code is
EnsembleTR
--ref ${ref_fa}
--out ${EnsembleTR_dir}/EnsembleTR_merge.chr${CHR}.vcf
--vcfs ${GangSTR},${ExpansionHunter},${HipSTR},${adVNTR}
I utilized call level and locus level filter prior to EnsembleTR, like this

call level filter

for GangSTR add more

basename=$(basename "${GangSTR_vcf}" .vcf.gz)
dumpSTR --vcf ${GangSTR_vcf} --out ${out_dir}/GangSTR/${basename}
--gangstr-min-call-DP 10 --gangstr-max-call-DP 1000 --gangstr-filter-spanbound-only --gangstr-filter-badCI --gangstr-min-call-Q 0.90

For ExpansionHunter

basename=$(basename "${ExpansionHunter_vcf}" .vcf.gz)
dumpSTR --vcf ${ExpansionHunter_vcf} --out ${out_dir}/ExpansionHunter/${basename}
--eh-min-call-LC 10 --eh-max-call-LC 1000

For HipSTR

basename=$(basename "${HipSTR_vcf}" .vcf.gz)
dumpSTR --vcf ${HipSTR_vcf} --out ${out_dir}/HipSTR/${basename}
--hipstr-min-call-Q 0.9 --hipstr-max-call-flank-indel 0.15 --hipstr-max-call-stutter 0.15 --hipstr-min-call-DP 10 --hipstr-max-call-DP 1000

adVNTR

basename=$(basename "${adVNTR_vcf}" .vcf.gz)
dumpSTR --vcf ${adVNTR_vcf} --out ${out_dir}/adVNTR/${basename}
--advntr-min-call-DP 10 --advntr-min-spanning 2 --advntr-min-flanking 2

locus level filter

conda activate flair
tools_list=('GangSTR' 'HipSTR')
work_dir=/qitinglab/shenlongxin/Fetal_GTEx/01_TR_Genotyping/STR_res/merge_vcf
cd ${work_dir}
tool=${tools_list[$SLURM_ARRAY_TASK_ID]}
bcftools sort -Oz -o ${work_dir}/${tool}_merge.sorted.vcf.gz ${work_dir}/${tool}_merge.vcf
tabix -p vcf ${work_dir}/${tool}_merge.sorted.vcf.gz
conda deactivate
conda activate EnsembleTR
dumpSTR --vcf ${work_dir}/${tool}_merge.sorted.vcf.gz --out ${tool}_merge.filter.vcf --min-locus-callrate 0.8 --min-locus-hwep 0.000001 --filter-regions /qitinglab/shenlongxin/Fetal_GTEx/01_TR_Genotyping/hg38_segdup.sorted.bed.gz --filter-regions-names SEGDUP
conda deactivate
conda activate flair
bcftools view -f PASS ${tool}_merge.filter.vcf | bcftools sort -Oz -o ${tool}_merge.filter.sorted.PASS.vcf.gz
tabix -p vcf ${tool}_merge.filter.sorted.PASS.vcf.gz

What suggestions can you give me to identify what errors occurred during the process? I look forward to and greatly appreciate your reply.