no output

[robertosirica]

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.