Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/bfd0706660cab959a85303f7245299/.command.sh
Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260511_LH00527_0083_A23TNVHLT4__8afaba2b--20260513-165037/alignments/recalibrated/1136_8DR-T1-TDNA-1_A23TNVHLT4_1/1136_8DR-T1-TDNA-1_A23TNVHLT4_1.recalibrated.bam
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260511_LH00527_0083_A23TNVHLT4__8afaba2b--20260513-165037/alignments/recalibrated/1136_8DR-T1-TDNA-1_A23TNVHLT4_1/1136_8DR-T1-TDNA-1_A23TNVHLT4_1.recalibrated.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/b6bfd04cf8e0046cc54e98c4afebf9/1136_8DR-T1-TDNA-1_A23TNVHLT4_1_vs_1136_8DR-N1-BDNA-1_A23NLN3LT4_1.snv_indel.merged.vcf.gz.tbi
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/b6bfd04cf8e0046cc54e98c4afebf9/1136_8DR-T1-TDNA-1_A23TNVHLT4_1_vs_1136_8DR-N1-BDNA-1_A23NLN3LT4_1.snv_indel.merged.vcf.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/bfd0706660cab959a85303f7245299/.command.run
==> STAGING COMPLETE (8 inputs)
[W::hts_idx_load3] The index file is older than the data file: 1136_8DR-T1-TDNA-1_A23TNVHLT4_1_vs_1136_8DR-N1-BDNA-1_A23NLN3LT4_1.snv_indel.merged.vcf.gz.tbi
This is WhatsHap 2.8 running under Python 3.9.23
[W::hts_idx_load3] The index file is older than the data file: 1136_8DR-T1-TDNA-1_A23TNVHLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_8DR-T1-TDNA-1_A23TNVHLT4_1.recalibrated.bam.bai
[E::idx_find_and_load] Could not retrieve index file for 'input_filtered.vcf.gz'
[E::idx_find_and_load] Could not retrieve index file for 'input_filtered.vcf.gz'
[E::idx_find_and_load] Could not retrieve index file for 'input_filtered.vcf.gz'
Working on 2 samples from 2 families
WARNING: Skipping duplicated position 15042898 on chromosome 'chr3' Hiding further warnings of this type, use --debug to show
# Working on contig chr3 in individual 1136_8DR-N1-BDNA-1_A23NLN3LT4_1
Found 3 usable heterozygous variants (0 skipped due to missing genotypes)
WARNING: Sample '1136_8DR-N1-BDNA-1_A23NLN3LT4_1' not found in any BAM/CRAM file.
Found 0 reads covering 0 variants
Kept 0 reads that cover at least two variants each
Selected 0 most phase-informative reads covering 0 variants
Best-case phasing would result in 0 non-singleton phased blocks (0 singletons).
Phasing 1 sample by solving the MEC problem ...
No. of phased blocks: 0
# Working on contig chr3 in individual 1136_8DR-T1-TDNA-1_A23TNVHLT4_1
Found 971 usable heterozygous variants (0 skipped due to missing genotypes)
[W::hts_idx_load3] The index file is older than the data file: 1136_8DR-T1-TDNA-1_A23TNVHLT4_1.recalibrated.bam.bai
Number of supplementary alignments: 0
Number of non-singleton groups: 64919
Skipped 0 groups
Found 253636 reads covering 971 variants
Kept 42563 reads that cover at least two variants each
Selected 1827 most phase-informative reads covering 376 variants
Best-case phasing would result in 119 non-singleton phased blocks (0 singletons).
Phasing 1 sample by solving the MEC problem ...
Largest block contains 20 variants (5.3% of accessible variants) between position 75741176 and 75741859
WARNING: Ignoring existing phasing information found in input VCF (PS tag exists).
# Resource usage
Maximum memory usage: 0.535 GB
Time spent reading BAM/CRAM: 241.8 s
Time spent parsing VCF: 0.0 s
Time spent selecting reads: 1.6 s
Time spent phasing: 1.0 s
Time spent writing VCF: 0.0 s
Time spent finding components: 0.0 s
Time spent on rest: 0.3 s
Total elapsed time: 244.7 s