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/de/2026cf0da888f4c786704dea3f03ad/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/1d4ab20980f8d731eb1f1cf3684bf8/1029_01F-T1-TDNA-1_A23TNVYLT4_1_vs_1029_01F-N1-BDNA-1_B23KFG5LT4_1.snv_indel.merged.vcf.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/1d4ab20980f8d731eb1f1cf3684bf8/1029_01F-T1-TDNA-1_A23TNVYLT4_1_vs_1029_01F-N1-BDNA-1_B23KFG5LT4_1.snv_indel.merged.vcf.gz.tbi
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/20260504_LH00527_0081_A23TNVYLT4__c86dea0e--20260506-131012/alignments/recalibrated/1029_01F-T1-TDNA-1_A23TNVYLT4_1/1029_01F-T1-TDNA-1_A23TNVYLT4_1.recalibrated.bam
Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260504_LH00527_0081_A23TNVYLT4__c86dea0e--20260506-131012/alignments/recalibrated/1029_01F-T1-TDNA-1_A23TNVYLT4_1/1029_01F-T1-TDNA-1_A23TNVYLT4_1.recalibrated.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/2026cf0da888f4c786704dea3f03ad/.command.run
==> STAGING COMPLETE (8 inputs)
[W::hts_idx_load3] The index file is older than the data file: 1029_01F-T1-TDNA-1_A23TNVYLT4_1_vs_1029_01F-N1-BDNA-1_B23KFG5LT4_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: 1029_01F-T1-TDNA-1_A23TNVYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_01F-T1-TDNA-1_A23TNVYLT4_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 23080170 on chromosome 'chr14' Hiding further warnings of this type, use --debug to show
# Working on contig chr14 in individual 1029_01F-N1-BDNA-1_B23KFG5LT4_1
Found 2 usable heterozygous variants (0 skipped due to missing genotypes)
WARNING: Sample '1029_01F-N1-BDNA-1_B23KFG5LT4_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 chr14 in individual 1029_01F-T1-TDNA-1_A23TNVYLT4_1
Found 1372 usable heterozygous variants (0 skipped due to missing genotypes)
[W::hts_idx_load3] The index file is older than the data file: 1029_01F-T1-TDNA-1_A23TNVYLT4_1.recalibrated.bam.bai
Number of supplementary alignments: 0
Number of non-singleton groups: 78871
Skipped 0 groups
Found 223589 reads covering 1372 variants
Kept 98076 reads that cover at least two variants each
Selected 2052 most phase-informative reads covering 1053 variants
Best-case phasing would result in 84 non-singleton phased blocks (0 singletons).
Phasing 1 sample by solving the MEC problem ...
Largest block contains 460 variants (43.7% of accessible variants) between position 104941894 and 104953399
WARNING: Ignoring existing phasing information found in input VCF (PS tag exists).
# Resource usage
Maximum memory usage: 0.361 GB
Time spent reading BAM/CRAM: 99.8 s
Time spent parsing VCF: 0.0 s
Time spent selecting reads: 3.9 s
Time spent phasing: 2.8 s
Time spent writing VCF: 0.1 s
Time spent finding components: 0.0 s
Time spent on rest: 0.8 s
Total elapsed time: 107.4 s