Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_7KK-N1-BDNA-1_A23NLN3LT4_1/1136_7KK-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/9b2d769e20f54fc33eb420e0926e49/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/9b2d769e20f54fc33eb420e0926e49/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_7KK-N1-BDNA-1_A23NLN3LT4_1/1136_7KK-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_7KK-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7KK-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_7KK-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7KK-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 97370858 total, 66672 skipped (flags/unmapped)
Fragments: 48777674 total (48484456 tlen-paired, 4843 hash-paired, 406 singletons, 16705 discordant, 271264 orphans, 10254 too large [>5000 bp], 17005457 duplicates)
Reads: 104739952 total, 59382 skipped (flags/unmapped)
Fragments: 52474659 total (52146503 tlen-paired, 6151 hash-paired, 364 singletons, 14331 discordant, 307310 orphans, 19463 too large [>5000 bp], 18474521 duplicates)
Reads: 105376537 total, 57015 skipped (flags/unmapped)
Fragments: 52787271 total (52491139 tlen-paired, 3819 hash-paired, 474 singletons, 11747 discordant, 280092 orphans, 12773 too large [>5000 bp], 18150486 duplicates)
Reads: 115347386 total, 97033 skipped (flags/unmapped)
Fragments: 57865463 total (57123360 tlen-paired, 2818 hash-paired, 387 singletons, 141406 discordant, 597492 orphans, 58653 too large [>5000 bp], 20423284 duplicates)