Errors about the hoobari software

[JIAYUREN000]

Dear professor Shomron,

We recently read your paper entitled "Bayesian-based noninvasive prenatal diagnosis of single-gene disorders" and used the hoobari software to predict fetal genotype using cfDNA and parental sequencing data. We consistently faced errors and couldn't perform the analysis. Would you please tell us how to solve this problem? Any suggestion will be deeply appreciated.

Jia

The command used was presented below
(base) [lijia3@cngb-login-0-18 hoobari-master]$ python src/hoobari_main.py -parents_vcf parents_chr1.vcf -cfdna_vcf cfDNA.output-hc_chr1.vcf -% 0.04 -cfdna_bam /zfssz6/ST_MCHRI/BIGDATA/P17Z10200N0306/1tube_sentieon_Backup2_back/JK-53_re/cfDNA/merge/cfDNA.recaled.bam -t /zfssz4/BC_RD_P2/USER/lijia3/Onetube/Bayes_model/Indels/hoobari-master/tmp_hb -f infer.vcf
pre-processing calculating error rate (a place holder is temporarily set to 0.003)
pre-processing creating length distributions
total fetal fraction: 0.04
pre-processing calculating an empirical distribution of fetal fractions per fragment length
0.04
##fileformat=VCFv4.1
##fileDate=20210826
##source=hoobari
##phasing=none
##reference=/zfssz2/ST_MCHRI/REPRO/Pipeline/Share_Pipe/DNA_human/Bin/database/hg19/index_fa/hg19.fasta
##commandline="src/hoobari_main.py -parents_vcf parents_chr1.vcf -cfdna_vcf cfDNA.output-hc_chr1.vcf -% 0.04 -cfdna_bam /zfssz6/ST_MCHRI/BIGDATA/P17Z10200N0306/1tube_sentieon_Backup2_back/JK-53_re/cfDNA/merge/cfDNA.recaled.bam -t /zfssz4/BC_RD_P2/USER/lijia3/Onetube/Bayes_model/Indels/hoobari-master/tmp_hb -f infer.vcf"

##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype",Source="hoobari">
##FORMAT=<ID=DP,Number=1,Type=String,Description="Read Depth">
##FORMAT=<ID=AD,Number=R,Type=String,Description="Number of observation for each allele">
##FORMAT=<ID=RO,Number=1,Type=String,Description="Reference allele observation count">
##FORMAT=<ID=QR,Number=1,Type=String,Description="Sum of quality of the reference observations">
##FORMAT=<ID=AO,Number=A,Type=String,Description="Alternate allele observation count">
##FORMAT=<ID=QA,Number=A,Type=String,Description="Sum of quality of the alternate observations">
##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy",Source="hoobari">
##FORMAT=<ID=PG,Number=G,Type=Float,Description="P(Genotype), Per-site genotype prior probabilities",Source="hoobari">
##FORMAT=<ID=PP,Number=G,Type=Float,Description="P(Posterior), Per-site genotype posterior probabilities",Source="hoobari">
##INFO=<ID=MGT,Number=1,Type=String,Description="Mother' Genotype">
##INFO=<ID=MGQ,Number=1,Type=Float,Description="Mother's Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
##INFO=<ID=MGL,Number=G,Type=Float,Description="Mother's Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
##INFO=<ID=MAD,Number=R,Type=Integer,Description="Mother's Number of observation for each allele">
##INFO=<ID=MDP,Number=1,Type=Integer,Description="Mother's Read Depth">
##INFO=<ID=MRO,Number=1,Type=Integer,Description="Mother's Reference allele observation count">
##INFO=<ID=MQR,Number=1,Type=Integer,Description="Mother's Sum of quality of the reference observations">
##INFO=<ID=MAO,Number=A,Type=Integer,Description="Mother's Alternate allele observation count">
##INFO=<ID=MQA,Number=A,Type=Integer,Description="Mother's Sum of quality of the alternate observations">
##INFO=<ID=FGT,Number=1,Type=String,Description="Father's Genotype">
##INFO=<ID=FGQ,Number=1,Type=Float,Description="Father's Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
##INFO=<ID=FGL,Number=G,Type=Float,Description="Father's Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
##INFO=<ID=FAD,Number=R,Type=Integer,Description="Father's Number of observation for each allele">
##INFO=<ID=FDP,Number=1,Type=Integer,Description="Father's Read Depth">
##INFO=<ID=FRO,Number=1,Type=Integer,Description="Father's Reference allele observation count">
##INFO=<ID=FQR,Number=1,Type=Integer,Description="Father's Sum of quality of the reference observations">
##INFO=<ID=FAO,Number=A,Type=Integer,Description="Father's Alternate allele observation count">
##INFO=<ID=FQA,Number=A,Type=Integer,Description="Father's Sum of quality of the alternate observations">
##INFO=<ID=MFQ,Number=1,Type=Float,Description="Mother's and Father's QUAL score from the parental vcf">
Traceback (most recent call last):
File "src/hoobari_main.py", line 77, in
output_path = args.vcf_output)
File "/zfssz4/BC_RD_P2/USER/lijia3/Onetube/Bayes_model/Indels/hoobari-master/src/vcf_out.py", line 104, in make_header
parents_vcf_infos_list = [line.strip() for line in f if line.startswith(b'##INFO')]
File "/zfssz4/BC_RD_P2/USER/lijia3/Onetube/Bayes_model/Indels/hoobari-master/src/vcf_out.py", line 104, in
parents_vcf_infos_list = [line.strip() for line in f if line.startswith(b'##INFO')]
TypeError: startswith first arg must be str or a tuple of str, not bytes