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PacificBiosciences / HiPhase

Small variant, structural variant, and short tandem repeat phasing tool for PacBio HiFi reads
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[Question] Phasing of rs36056539 in NA19226 #34

Closed davidyuyuan closed 6 months ago

davidyuyuan commented 6 months ago

rs36056539 shows in trans with rs3745274 and rs2279343 from the BAM for NA19226 from the Twist Alliance Long Read PGx Panel. In your publication, https://www.pacb.com/wp-content/uploads/2023-03_PGx_Poster_Hybrid-Capture_FINAL.pdf, 18/20 was called. This means rs36056539, rs3745274 and rs2279343 should be in cis for *20. Can you please comment on whether rs36056539 should be in cis or in trans?

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  NA19226
chr19   41006923    rs36056539  C   T   222.381 PASS    DP=184;VDB=0.183499;SGB=-0.693147;RPBZ=0.348212;MQBZ=0;MQSBZ=0;BQBZ=2.13977;SCBZ=-1.85906;MQ0F=0;AC=1;AN=2;DP4=46,40,40,58;MQ=60    GT:PL:PS    0|1:255,0,255:40991670
chr19   41006936    rs3745274   G   T   222.375 PASS    DP=183;VDB=0.576103;SGB=-0.693147;RPBZ=-0.750617;MQBZ=0;MQSBZ=0;BQBZ=-0.667956;SCBZ=1.08562;MQ0F=0;AC=1;AN=2;DP4=41,58,45,39;MQ=60  GT:PL:PS    1|0:255,0,255:40991670
chr19   41009358    rs2279343   A   G   222.406 PASS    DP=138;VDB=0.87811;SGB=-0.693147;RPBZ=-1.75911;MQBZ=0;MQSBZ=0;BQBZ=-0.625866;SCBZ=0;MQ0F=0;AC=1;AN=2;DP4=29,39,34,36;MQ=60  GT:PL:PS    1|0:255,0,255:40991670
chr19   41012316    rs28399499  T   C   222.382 PASS    DP=138;VDB=0.999793;SGB=-0.693147;RPBZ=-1.3622;MQBZ=0;MQSBZ=0;BQBZ=0.305764;SCBZ=0;MQ0F=0;AC=1;AN=2;DP4=25,49,37,27;MQ=60   GT:PL:PS    0|1:255,0,255:40991670

Just FYI, here are the options used when HiPhase was called:

/opt/conda/bin/hiphase --bam "${output_dir}/${file}.smaller.bam" --vcf "${output_dir}/${file}.unphased.vcf.gz" --output-vcf "${vcf_file}" --reference "${ref_genome}" --threads 16
davidyuyuan commented 6 months ago

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
holtjma commented 6 months ago

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:

igv_snapshot

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:

  1. 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.
  2. 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

davidyuyuan commented 6 months ago

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!