nshomron/hoobari

Bayesian-based fetal genotyping using maternal cell-free DNA and parental sequencing data.

hoobari's Issues

Errors about the hoobari software

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

Hoobari installation problem

Hello, I'm trying to install hoobari after downloading it as stated in the manual page but it gives me this error:

/usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'install_requires'
warnings.warn(msg)
running install
running build
running build_py
package init file 'src/init.py' not found (or not a regular file)
package init file 'src/init.py' not found (or not a regular file)
running build_ext
building 'phred' extension
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-J8eN0k/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/usr/include/python2.7 -c src/phred.c -o build/temp.linux-x86_64-2.7/src/phred.o
x86_64-linux-gnu-gcc: error: src/phred.c: File o directory non esistente
x86_64-linux-gnu-gcc: fatal error: no input files
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

thank you

no output

Hello Dr. Rabinowitz, , I just managed to perform step 2 (Pre-processing of cfDNA:) and it prints me on the screen a lot of lines like these:

found genotype alleles
filtering genotype alleles which are not supported by at least 2 observations comprising at least 0.05000 of the observations in a single individual
genotype allele: reference:47M:460:1:C qsum 36
genotype allele: snp:1M1X:460:1:CG qsum 15
filtered genotype alleles
evaluating input allele snp:1X:460:1:G
fitting haplotype block 460 to 461, 1bp
got complete observations of haplotype
added to registered alleles
got partial observations of haplotype
done updating
refr_seq 460 C
haplo_obs 460 -3.22362 C default:NDX550231_RUO:19:HJKWKAFXY:1:11303:19089:1717:reference:1:1:460:+:C:461:1M:-13.8:-3.2
haplo_obs 460 -8.28931 C default:NDX550231_RUO:19:HJKWKAFXY:1:11303:19089:1717:reference:1:1:460:-:C:410:1M:-13.8:-8.3
getting genotype alleles
allele group C
default:NDX550231_RUO:19:HJKWKAFXY:1:11303:19089:1717:reference:1:1:460:+:C:461:1M:-13.8:-3.2|default:NDX550231_RUO:19:HJKWKAFXY:1:11303:19089:1717:reference:1:1:460:-:C:410:1M:-13.8:-8.3

and other like this:
input allele: snp:1X:173797504:1:T
input allele: snp:1X:173797507:1:G
input allele: snp:1X:173797508:1:G
input allele: snp:1X:173797509:1:G
input allele: snp:1X:173797511:1:G
input allele: snp:1X:173797512:1:G
input allele: snp:1X:173797513:1:G
input allele: snp:1X:173797514:1:T
input allele: snp:1X:173797515:1:G
input allele: snp:1X:173797517:1:G
input allele: snp:1X:173797518:1:G
input allele: snp:1X:173797519:1:G
input allele: snp:1X:173797519:1:T

I understand that these lines are the progress state database building.

At the end appeared a temp_hb directory in which there is hoobari.db file in sql format, so I moved on to the third step as outlined in the online manual repeating exactly the specified command line, i.e. :

hoobari
-parents_vcf parents.vcf
-cfdna_vcf cfdna.vcf

Is cfdna.vcf the result file to specify?

this command prints me out these lines:

pre-processing creating length distributions
/root/~/tmp_hb/hoobari.db

but no output is created nor any error message printed on screen.

Thanks.