Problems with hs37d5 reference. #1
Description
Just started testing the navigator and ran in to this issue. The resulting VCF has only a header.
[info] [ViewModel] Starting YDNA haplogroup analysis for hs37d5_mem2.bam
[info] Found ftdna-ytree in disk cache. Parsing...
[info] Caching parsed tree in memory for ftdna-ytree.
[info] Found reference GRCh38 in cache: /home/user/references/hg38.fa
[info] Downloading chain file from http://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/hg38ToHg19.over.chain.gz
[info] Download complete. Caching chain file.
[info] Found reference GRCh37 in cache: /home/user/references/hs37d5.fa
[error] INFO 2025-12-11 18:10:41 LiftoverVcf Loading up the target reference genome.
[error] INFO 2025-12-11 18:10:49 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.)
[error] WARNING 2025-12-11 18:10:49 LiftoverVcf Encountered a contig, chrY that is not part of the target reference.
[error] WARNING 2025-12-11 18:10:49 LiftoverVcf Encountered a contig, chrY that is not part of the target reference.
[error] WARNING 2025-12-11 18:10:49 LiftoverVcf Encountered a contig, chrY that is not part of the target reference.
[error] WARNING 2025-12-11 18:10:49 LiftoverVcf Encountered a contig, chrY that is not part of the target reference.
[error] WARNING 2025-12-11 18:10:49 LiftoverVcf Encountered a contig, chrY that is not part of the target reference.
[error] WARNING 2025-12-11 18:10:49 LiftoverVcf Encountered a contig, chrY that is not part of the target reference.
[error] WARNING 2025-12-11 18:10:49 LiftoverVcf Encountered a contig, chrY that is not part of the target reference.removed similar lines
[info] [HaplogroupProcessor] Cached lifted sites VCF to /home/user/.decodingus/cache/trees/ftdna-ytree-path-R-U152-GRCh38-to-GRCh37-sites.vcf
[error] WARNING 2025-12-11 18:10:49 LiftoverVcf Encountered a contig, chrY that is not part of the target reference.
[error] WARNING 2025-12-11 18:10:49 LiftoverVcf Encountered a contig, chrY that is not part of the target reference.removed similar lines
[error] WARNING 2025-12-11 18:10:49 LiftoverVcf Encountered a contig, chrY that is not part of the target reference.
[error] WARNING 2025-12-11 18:10:49 LiftoverVcf Encountered a contig, chrY that is not part of the target reference.
[error] WARNING 2025-12-11 18:10:49 LiftoverVcf Encountered a contig, chrY that is not part of the target reference.
[info] [HaplogroupProcessor] Saved lifted alleles VCF to /home/user/.decodingus/cache/subjects/28ce2cf3-03fd-4c01-91d4-7625d92d9d66/runs/7218272f/alignments/df5cef38/haplogroup/ydna_lifted_alleles_GRCh37.vcf
[info] Found reference GRCh37 in cache: /home/user/references/hs37d5.fa
[error] WARNING 2025-12-11 18:10:49 LiftoverVcf Encountered a contig, chrY that is not part of the target reference.
[error] WARNING 2025-12-11 18:10:49 LiftoverVcf Encountered a contig, chrY that is not part of the target reference.
[error] WARNING 2025-12-11 18:10:49 LiftoverVcf Encountered a contig, chrY that is not part of the target reference.
[error] WARNING 2025-12-11 18:10:49 LiftoverVcf Encountered a contig, chrY that is not part of the target reference.
[error] WARNING 2025-12-11 18:10:49 LiftoverVcf Encountered a contig, chrY that is not part of the target reference.
[error] INFO 2025-12-11 18:10:49 LiftoverVcf Processed 1847 variants.
[error] INFO 2025-12-11 18:10:49 LiftoverVcf 1847 variants failed to liftover.
[error] INFO 2025-12-11 18:10:49 LiftoverVcf 0 variants lifted over but had mismatching reference alleles after lift over.
[error] INFO 2025-12-11 18:10:49 LiftoverVcf 100.0000% of variants were not successfully lifted over and written to the output.
[error] INFO 2025-12-11 18:10:49 LiftoverVcf liftover success by source contig:
[error] INFO 2025-12-11 18:10:49 LiftoverVcf chrY: 0 / 1847 (0.0000%)
[error] INFO 2025-12-11 18:10:49 LiftoverVcf lifted variants by target contig:
[error] INFO 2025-12-11 18:10:49 LiftoverVcf no successfully lifted variants
[error] INFO 2025-12-11 18:10:49 LiftoverVcf 0 variants were lifted by swapping REF/ALT alleles.
[error] INFO 2025-12-11 18:10:49 LiftoverVcf Writing out sorted records to final VCF.