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/16/4e89106e3e7f5966dd5852c446a4ac/.command.sh
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/2dcbe25583f0e66109a12acffebe53/1136_8DK-T1-TDNA-1_A23TNVYLT4_1_vs_1136_8DK-N1-BDNA-1_B23KFG5LT4_1.snv_indel.merged.vcf.gz.tbi
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/2dcbe25583f0e66109a12acffebe53/1136_8DK-T1-TDNA-1_A23TNVYLT4_1_vs_1136_8DK-N1-BDNA-1_B23KFG5LT4_1.snv_indel.merged.vcf.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/16/4e89106e3e7f5966dd5852c446a4ac/.command.run
Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260504_LH00527_0081_A23TNVYLT4__c86dea0e--20260506-131012/alignments/recalibrated/1136_8DK-T1-TDNA-1_A23TNVYLT4_1/1136_8DK-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/1136_8DK-T1-TDNA-1_A23TNVYLT4_1/1136_8DK-T1-TDNA-1_A23TNVYLT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (8 inputs)
[W::hts_idx_load3] The index file is older than the data file: 1136_8DK-T1-TDNA-1_A23TNVYLT4_1_vs_1136_8DK-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: 1136_8DK-T1-TDNA-1_A23TNVYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_8DK-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 16327684 on chromosome 'chr6' Hiding further warnings of this type, use --debug to show
# Working on contig chr6 in individual 1136_8DK-N1-BDNA-1_B23KFG5LT4_1
Found 175 usable heterozygous variants (0 skipped due to missing genotypes)
WARNING: Sample '1136_8DK-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 chr6 in individual 1136_8DK-T1-TDNA-1_A23TNVYLT4_1
Found 2000 usable heterozygous variants (0 skipped due to missing genotypes)
[W::hts_idx_load3] The index file is older than the data file: 1136_8DK-T1-TDNA-1_A23TNVYLT4_1.recalibrated.bam.bai
Number of supplementary alignments: 0
Number of non-singleton groups: 98430
Skipped 0 groups
Found 246517 reads covering 2000 variants
Kept 91089 reads that cover at least two variants each
Selected 2458 most phase-informative reads covering 1431 variants
Best-case phasing would result in 106 non-singleton phased blocks (0 singletons).
Phasing 1 sample by solving the MEC problem ...
Largest block contains 640 variants (44.7% of accessible variants) between position 29722917 and 31357755
WARNING: Ignoring existing phasing information found in input VCF (PS tag exists).
# Resource usage
Maximum memory usage: 0.516 GB
Time spent reading BAM/CRAM: 182.4 s
Time spent parsing VCF: 0.0 s
Time spent selecting reads: 3.2 s
Time spent phasing: 3.6 s
Time spent writing VCF: 0.1 s
Time spent finding components: 0.0 s
Time spent on rest: 0.9 s
Total elapsed time: 190.2 s