Comments (3)
Thank you, Matt, for the detailed analysis and explaination. I agree that HiPhase reported what it saw correctly. I should have thought about passing the BAM into a genome browser myself :)
I did not know that the BAM had gone through WhatsHap. I shortened it to the CYP2B6 gene region and passed it to HiPhase with my unphased VCF generated by bcftools mpileup / call / norm. In the end, I used the phased VCF to query the CPIC database and got *6/*18.
Thanks again!
from hiphase.
Here is a copy of the log:
[2024-04-30T17:38:15.643Z INFO hiphase::cli] Alignment file: "/home/jovyan/work/sunnybrook/results/NA19226/CYP2B6/actionable/GRCh38/NA19226.GRCh38_noalt.deepvariant.haplotagged.bam.smaller.bam"
[2024-04-30T17:38:15.643Z INFO hiphase::cli] Variant file: "/home/jovyan/work/sunnybrook/results/NA19226/CYP2B6/actionable/GRCh38/NA19226.GRCh38_noalt.deepvariant.haplotagged.bam.unphased.vcf.gz"
[2024-04-30T17:38:15.710Z INFO hiphase::cli] Reference file: "/home/jovyan/work/GRCh38/GRCh38_full_analysis_set_plus_decoy_hla.fa"
[2024-04-30T17:38:15.710Z INFO hiphase::cli] Variant filtering:
[2024-04-30T17:38:15.710Z INFO hiphase::cli] Minimum call quality: 0
[2024-04-30T17:38:15.710Z INFO hiphase::cli] Minimum mapping quality: 5
[2024-04-30T17:38:15.710Z INFO hiphase::cli] Minimum matched alleles: 2
[2024-04-30T17:38:15.710Z INFO hiphase::cli] Phase block generation:
[2024-04-30T17:38:15.710Z INFO hiphase::cli] Minimum spanning reads: 1
[2024-04-30T17:38:15.710Z INFO hiphase::cli] Supplemental mapping block joins: ENABLED
[2024-04-30T17:38:15.710Z INFO hiphase::cli] Phase singleton blocks: DISABLED
[2024-04-30T17:38:15.710Z INFO hiphase::cli] Allele assignment:
[2024-04-30T17:38:15.710Z INFO hiphase::cli] Local re-alignment maximum reference buffer: +-15 bp
[2024-04-30T17:38:15.710Z INFO hiphase::cli] Global re-alignment max edit distance: 500
[2024-04-30T17:38:15.710Z INFO hiphase::cli] Global prune distance: 500
[2024-04-30T17:38:15.710Z INFO hiphase::cli] Processing threads: 16
[2024-04-30T17:38:15.710Z INFO hiphase::cli] I/O threads: 4
[2024-04-30T17:38:15.946Z INFO hiphase::data_types::reference_genome] Loading "/home/jovyan/work/GRCh38/GRCh38_full_analysis_set_plus_decoy_hla.fa"...
[2024-04-30T17:38:42.327Z INFO hiphase::data_types::reference_genome] Finished loading 3366 contigs.
[2024-04-30T17:38:42.429Z INFO hiphase] Phase block generation starting...
[2024-04-30T17:38:42.429Z INFO hiphase] Starting job pool with 16 threads...
[2024-04-30T17:38:42.442Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr1":0 in indexed file', while seeking to chr1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:42.443Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr2":0 in indexed file', while seeking to chr2:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:42.443Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr3":0 in indexed file', while seeking to chr3:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:42.443Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr4":0 in indexed file', while seeking to chr4:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:42.443Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr5":0 in indexed file', while seeking to chr5:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:42.443Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr6":0 in indexed file', while seeking to chr6:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:42.443Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr7":0 in indexed file', while seeking to chr7:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:42.443Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr8":0 in indexed file', while seeking to chr8:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:42.443Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr9":0 in indexed file', while seeking to chr9:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:42.443Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr10":0 in indexed file', while seeking to chr10:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:42.443Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr11":0 in indexed file', while seeking to chr11:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:42.443Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr12":0 in indexed file', while seeking to chr12:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:42.443Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr13":0 in indexed file', while seeking to chr13:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:42.443Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr14":0 in indexed file', while seeking to chr14:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:42.443Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr15":0 in indexed file', while seeking to chr15:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:42.443Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr16":0 in indexed file', while seeking to chr16:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:42.629Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr17":0 in indexed file', while seeking to chr17:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:42.629Z INFO hiphase] Generated 100 phase blocks, latest block: PhaseBlock { block_index: 99, coordinates: "chrUn_KI270509v1:0-0", num_variants: 0, sample_name: "NA19226" }
[2024-04-30T17:38:42.629Z INFO hiphase] Received results for 100 phase blocks: 498.1950 blocks/sec, 0.0000 hets/sec, writer waiting on block 18
[2024-04-30T17:38:43.480Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr18":0 in indexed file', while seeking to chr18:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.489Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr20":0 in indexed file', while seeking to chr20:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.489Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr21":0 in indexed file', while seeking to chr21:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.489Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr22":0 in indexed file', while seeking to chr22:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.489Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrX":0 in indexed file', while seeking to chrX:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.489Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrY":0 in indexed file', while seeking to chrY:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.489Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrM":0 in indexed file', while seeking to chrM:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.489Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr1_KI270706v1_random":0 in indexed file', while seeking to chr1_KI270706v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.489Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr1_KI270707v1_random":0 in indexed file', while seeking to chr1_KI270707v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.489Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr1_KI270708v1_random":0 in indexed file', while seeking to chr1_KI270708v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.489Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr1_KI270709v1_random":0 in indexed file', while seeking to chr1_KI270709v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.489Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr1_KI270710v1_random":0 in indexed file', while seeking to chr1_KI270710v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.489Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr1_KI270711v1_random":0 in indexed file', while seeking to chr1_KI270711v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.489Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr1_KI270712v1_random":0 in indexed file', while seeking to chr1_KI270712v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.489Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr1_KI270713v1_random":0 in indexed file', while seeking to chr1_KI270713v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.489Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr1_KI270714v1_random":0 in indexed file', while seeking to chr1_KI270714v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.489Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr2_KI270715v1_random":0 in indexed file', while seeking to chr2_KI270715v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr2_KI270716v1_random":0 in indexed file', while seeking to chr2_KI270716v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr3_GL000221v1_random":0 in indexed file', while seeking to chr3_GL000221v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr4_GL000008v2_random":0 in indexed file', while seeking to chr4_GL000008v2_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr5_GL000208v1_random":0 in indexed file', while seeking to chr5_GL000208v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr9_KI270717v1_random":0 in indexed file', while seeking to chr9_KI270717v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr9_KI270718v1_random":0 in indexed file', while seeking to chr9_KI270718v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr9_KI270719v1_random":0 in indexed file', while seeking to chr9_KI270719v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr9_KI270720v1_random":0 in indexed file', while seeking to chr9_KI270720v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr11_KI270721v1_random":0 in indexed file', while seeking to chr11_KI270721v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr14_GL000009v2_random":0 in indexed file', while seeking to chr14_GL000009v2_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr14_GL000225v1_random":0 in indexed file', while seeking to chr14_GL000225v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr14_KI270722v1_random":0 in indexed file', while seeking to chr14_KI270722v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr14_GL000194v1_random":0 in indexed file', while seeking to chr14_GL000194v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr14_KI270723v1_random":0 in indexed file', while seeking to chr14_KI270723v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr14_KI270724v1_random":0 in indexed file', while seeking to chr14_KI270724v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr14_KI270725v1_random":0 in indexed file', while seeking to chr14_KI270725v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr14_KI270726v1_random":0 in indexed file', while seeking to chr14_KI270726v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr15_KI270727v1_random":0 in indexed file', while seeking to chr15_KI270727v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr16_KI270728v1_random":0 in indexed file', while seeking to chr16_KI270728v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr17_GL000205v2_random":0 in indexed file', while seeking to chr17_GL000205v2_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr17_KI270729v1_random":0 in indexed file', while seeking to chr17_KI270729v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr17_KI270730v1_random":0 in indexed file', while seeking to chr17_KI270730v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr22_KI270731v1_random":0 in indexed file', while seeking to chr22_KI270731v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr22_KI270732v1_random":0 in indexed file', while seeking to chr22_KI270732v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr22_KI270733v1_random":0 in indexed file', while seeking to chr22_KI270733v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr22_KI270734v1_random":0 in indexed file', while seeking to chr22_KI270734v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr22_KI270735v1_random":0 in indexed file', while seeking to chr22_KI270735v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr22_KI270736v1_random":0 in indexed file', while seeking to chr22_KI270736v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr22_KI270737v1_random":0 in indexed file', while seeking to chr22_KI270737v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr22_KI270738v1_random":0 in indexed file', while seeking to chr22_KI270738v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chr22_KI270739v1_random":0 in indexed file', while seeking to chr22_KI270739v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrY_KI270740v1_random":0 in indexed file', while seeking to chrY_KI270740v1_random:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270302v1":0 in indexed file', while seeking to chrUn_KI270302v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270304v1":0 in indexed file', while seeking to chrUn_KI270304v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270303v1":0 in indexed file', while seeking to chrUn_KI270303v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270305v1":0 in indexed file', while seeking to chrUn_KI270305v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270322v1":0 in indexed file', while seeking to chrUn_KI270322v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270320v1":0 in indexed file', while seeking to chrUn_KI270320v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270310v1":0 in indexed file', while seeking to chrUn_KI270310v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270316v1":0 in indexed file', while seeking to chrUn_KI270316v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270315v1":0 in indexed file', while seeking to chrUn_KI270315v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270312v1":0 in indexed file', while seeking to chrUn_KI270312v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270311v1":0 in indexed file', while seeking to chrUn_KI270311v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270317v1":0 in indexed file', while seeking to chrUn_KI270317v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270412v1":0 in indexed file', while seeking to chrUn_KI270412v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270411v1":0 in indexed file', while seeking to chrUn_KI270411v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270414v1":0 in indexed file', while seeking to chrUn_KI270414v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270419v1":0 in indexed file', while seeking to chrUn_KI270419v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270418v1":0 in indexed file', while seeking to chrUn_KI270418v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270420v1":0 in indexed file', while seeking to chrUn_KI270420v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270424v1":0 in indexed file', while seeking to chrUn_KI270424v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270417v1":0 in indexed file', while seeking to chrUn_KI270417v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270422v1":0 in indexed file', while seeking to chrUn_KI270422v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270423v1":0 in indexed file', while seeking to chrUn_KI270423v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270425v1":0 in indexed file', while seeking to chrUn_KI270425v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270429v1":0 in indexed file', while seeking to chrUn_KI270429v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270442v1":0 in indexed file', while seeking to chrUn_KI270442v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270466v1":0 in indexed file', while seeking to chrUn_KI270466v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270465v1":0 in indexed file', while seeking to chrUn_KI270465v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270467v1":0 in indexed file', while seeking to chrUn_KI270467v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270435v1":0 in indexed file', while seeking to chrUn_KI270435v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270438v1":0 in indexed file', while seeking to chrUn_KI270438v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270468v1":0 in indexed file', while seeking to chrUn_KI270468v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270510v1":0 in indexed file', while seeking to chrUn_KI270510v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270509v1":0 in indexed file', while seeking to chrUn_KI270509v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270518v1":0 in indexed file', while seeking to chrUn_KI270518v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270508v1":0 in indexed file', while seeking to chrUn_KI270508v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270516v1":0 in indexed file', while seeking to chrUn_KI270516v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270512v1":0 in indexed file', while seeking to chrUn_KI270512v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270519v1":0 in indexed file', while seeking to chrUn_KI270519v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270522v1":0 in indexed file', while seeking to chrUn_KI270522v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270511v1":0 in indexed file', while seeking to chrUn_KI270511v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270515v1":0 in indexed file', while seeking to chrUn_KI270515v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270507v1":0 in indexed file', while seeking to chrUn_KI270507v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270517v1":0 in indexed file', while seeking to chrUn_KI270517v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270529v1":0 in indexed file', while seeking to chrUn_KI270529v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270528v1":0 in indexed file', while seeking to chrUn_KI270528v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270530v1":0 in indexed file', while seeking to chrUn_KI270530v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270539v1":0 in indexed file', while seeking to chrUn_KI270539v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270538v1":0 in indexed file', while seeking to chrUn_KI270538v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270544v1":0 in indexed file', while seeking to chrUn_KI270544v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270548v1":0 in indexed file', while seeking to chrUn_KI270548v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270583v1":0 in indexed file', while seeking to chrUn_KI270583v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270587v1":0 in indexed file', while seeking to chrUn_KI270587v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270580v1":0 in indexed file', while seeking to chrUn_KI270580v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270581v1":0 in indexed file', while seeking to chrUn_KI270581v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270579v1":0 in indexed file', while seeking to chrUn_KI270579v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270589v1":0 in indexed file', while seeking to chrUn_KI270589v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270590v1":0 in indexed file', while seeking to chrUn_KI270590v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270584v1":0 in indexed file', while seeking to chrUn_KI270584v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270582v1":0 in indexed file', while seeking to chrUn_KI270582v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270588v1":0 in indexed file', while seeking to chrUn_KI270588v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270593v1":0 in indexed file', while seeking to chrUn_KI270593v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270591v1":0 in indexed file', while seeking to chrUn_KI270591v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270330v1":0 in indexed file', while seeking to chrUn_KI270330v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270329v1":0 in indexed file', while seeking to chrUn_KI270329v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270334v1":0 in indexed file', while seeking to chrUn_KI270334v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270333v1":0 in indexed file', while seeking to chrUn_KI270333v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270335v1":0 in indexed file', while seeking to chrUn_KI270335v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270338v1":0 in indexed file', while seeking to chrUn_KI270338v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270340v1":0 in indexed file', while seeking to chrUn_KI270340v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270336v1":0 in indexed file', while seeking to chrUn_KI270336v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270337v1":0 in indexed file', while seeking to chrUn_KI270337v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270363v1":0 in indexed file', while seeking to chrUn_KI270363v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270364v1":0 in indexed file', while seeking to chrUn_KI270364v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270362v1":0 in indexed file', while seeking to chrUn_KI270362v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270366v1":0 in indexed file', while seeking to chrUn_KI270366v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270378v1":0 in indexed file', while seeking to chrUn_KI270378v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270379v1":0 in indexed file', while seeking to chrUn_KI270379v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270389v1":0 in indexed file', while seeking to chrUn_KI270389v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270390v1":0 in indexed file', while seeking to chrUn_KI270390v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270387v1":0 in indexed file', while seeking to chrUn_KI270387v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270395v1":0 in indexed file', while seeking to chrUn_KI270395v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270396v1":0 in indexed file', while seeking to chrUn_KI270396v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270388v1":0 in indexed file', while seeking to chrUn_KI270388v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270394v1":0 in indexed file', while seeking to chrUn_KI270394v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270386v1":0 in indexed file', while seeking to chrUn_KI270386v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270391v1":0 in indexed file', while seeking to chrUn_KI270391v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270383v1":0 in indexed file', while seeking to chrUn_KI270383v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270393v1":0 in indexed file', while seeking to chrUn_KI270393v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270384v1":0 in indexed file', while seeking to chrUn_KI270384v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270392v1":0 in indexed file', while seeking to chrUn_KI270392v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270381v1":0 in indexed file', while seeking to chrUn_KI270381v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270385v1":0 in indexed file', while seeking to chrUn_KI270385v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270382v1":0 in indexed file', while seeking to chrUn_KI270382v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270376v1":0 in indexed file', while seeking to chrUn_KI270376v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270374v1":0 in indexed file', while seeking to chrUn_KI270374v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270372v1":0 in indexed file', while seeking to chrUn_KI270372v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270373v1":0 in indexed file', while seeking to chrUn_KI270373v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.490Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270375v1":0 in indexed file', while seeking to chrUn_KI270375v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.491Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270371v1":0 in indexed file', while seeking to chrUn_KI270371v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.491Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270448v1":0 in indexed file', while seeking to chrUn_KI270448v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.491Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270521v1":0 in indexed file', while seeking to chrUn_KI270521v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.491Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_GL000195v1":0 in indexed file', while seeking to chrUn_GL000195v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.491Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_GL000219v1":0 in indexed file', while seeking to chrUn_GL000219v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.491Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_GL000220v1":0 in indexed file', while seeking to chrUn_GL000220v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.491Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_GL000224v1":0 in indexed file', while seeking to chrUn_GL000224v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.491Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270741v1":0 in indexed file', while seeking to chrUn_KI270741v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.491Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_GL000226v1":0 in indexed file', while seeking to chrUn_GL000226v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.491Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_GL000213v1":0 in indexed file', while seeking to chrUn_GL000213v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.491Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270743v1":0 in indexed file', while seeking to chrUn_KI270743v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.491Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270744v1":0 in indexed file', while seeking to chrUn_KI270744v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.491Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270745v1":0 in indexed file', while seeking to chrUn_KI270745v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.491Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270746v1":0 in indexed file', while seeking to chrUn_KI270746v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.491Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270747v1":0 in indexed file', while seeking to chrUn_KI270747v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.491Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270748v1":0 in indexed file', while seeking to chrUn_KI270748v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.491Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270749v1":0 in indexed file', while seeking to chrUn_KI270749v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.491Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270750v1":0 in indexed file', while seeking to chrUn_KI270750v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.491Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270751v1":0 in indexed file', while seeking to chrUn_KI270751v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.491Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270752v1":0 in indexed file', while seeking to chrUn_KI270752v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.491Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270753v1":0 in indexed file', while seeking to chrUn_KI270753v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.491Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270754v1":0 in indexed file', while seeking to chrUn_KI270754v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.491Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270755v1":0 in indexed file', while seeking to chrUn_KI270755v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.491Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270756v1":0 in indexed file', while seeking to chrUn_KI270756v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.491Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270757v1":0 in indexed file', while seeking to chrUn_KI270757v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.491Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_GL000214v1":0 in indexed file', while seeking to chrUn_GL000214v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.491Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_KI270742v1":0 in indexed file', while seeking to chrUn_KI270742v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.491Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_GL000216v2":0 in indexed file', while seeking to chrUn_GL000216v2:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.491Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrUn_GL000218v1":0 in indexed file', while seeking to chrUn_GL000218v1:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.491Z INFO hiphase] Received results for 195 / 195 phase blocks: 183.5761 blocks/sec, 88.4931 hets/sec, writer waiting on block 195
[2024-04-30T17:38:43.491Z INFO hiphase] All phase blocks analyzed, finalizing output files...
[2024-04-30T17:38:43.491Z WARN hiphase::writers::ordered_vcf_writer] Received 'error seeking to "chrEBV":0 in indexed file', while seeking to chrEBV:0-18446744073709551615 in vcf #0, likely no variants present
[2024-04-30T17:38:43.630Z INFO hiphase] Finished building index for "/home/jovyan/work/sunnybrook/results/NA19226/CYP2B6/actionable/GRCh38/NA19226.GRCh38_noalt.deepvariant.haplotagged.bam.vcf.gz".
[2024-04-30T17:38:43.630Z INFO hiphase] All phase blocks finished successfully after 1.20131311 seconds.
Generated /home/jovyan/work/sunnybrook/results/NA19226/CYP2B6/actionable/GRCh38/NA19226.GRCh38_noalt.deepvariant.haplotagged.bam.vcf.gz
from hiphase.
Hi @davidyuyuan,
Let me just start by saying I can't speak to what NA19226 should be called, and I think there may be some ambiguity around it as well (more on that below).
First, let me address the HiPhase component: Looking at the BAM file you referenced, let me first point out that it was actually run with WhatsHap, I'm assuming you re-ran it with HiPhase locally. Second, I think it's pretty clear that rs36056539
and rs3745274
are in trans based on the existing WhatsHap BAM file:
Overall, this tells me that HiPhase is likely calling these particular variants correctly, and that this is not a HiPhase issue. Instead, I think this is a database issue:
- This dataset is part of a test sample we use for our PGx calling tool pb-StarPhase, which is under development. When we provide an unphased VCF to StarPhase, it will call *18/*20. However, if we provide a phased VCF (from HiPhase or WhatsHap, it doesn't matter), it will call
NO_MATCH/NO_MATCH
, which basically indicates that the phased entries do not produce a pair of haplotypes that exactly match something in the CPIC database. In other words, it is something else that is not described. - If you go look at the actual GeT-RM entry for this sample, it has
*18/(*20)
. I don't know what the parentheses indicates, but I believe it is meant to indicate some sort of ambiguity and/or disagreement. I would caution the precise usage of those calls from GeT-RM.
So overall, I think HiPhase is doing the right thing and that this dataset simply does not have a clean call for CYP2B6 at this time.
Matt
from hiphase.
Related Issues (20)
- Encountered max_edit_distance check HOT 6
- Recommendations for input vcf HOT 3
- A question about HP tag HOT 6
- reference letter case issue HOT 2
- Feature request: haplotag in phased VCF files HOT 2
- Running HiPhase with tumor-normal pair HOT 2
- Error while parsing VCF file: FORMAT columns HOT 3
- Expected memory usage HOT 3
- Phase vcf with pre phased reads HOT 6
- Normalization of INDELs: required or should be avoided HOT 3
- [Suggestion] reducing messages to STDOUT to speed up the utility HOT 3
- [Question] information in the filter column of vcfs HOT 2
- ERROR : 0 matched samples for phasing HOT 2
- possibility to utilize information from phased bam files HOT 4
- thread 'main' panicked error HOT 3
- gVCF + VCF processing HOT 6
- can the three output vcf directly concatenate? HOT 2
- Inconsistent Haplotype HOT 4
- how to deal with unphased variants in the output HOT 3
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from hiphase.