Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_TZ4-N1-BDNA-1_A23TNVNLT4_1/1241_TZ4-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/85af5adb586a5af8f2a75e1f029a18/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_TZ4-N1-BDNA-1_A23TNVNLT4_1/1241_TZ4-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  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/13/85af5adb586a5af8f2a75e1f029a18/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1241_TZ4-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_TZ4-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_TZ4-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_TZ4-N1-BDNA-1_A23TNVNLT4_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: 102771882 total, 74069 skipped (flags/unmapped)
Fragments: 51582592 total (51070655 tlen-paired, 3487 hash-paired, 470 singletons, 16927 discordant, 491053 orphans, 12076 too large [>5000 bp], 22099716 duplicates)
Reads: 110005630 total, 61694 skipped (flags/unmapped)
Fragments: 55225042 total (54681234 tlen-paired, 3286 hash-paired, 644 singletons, 11830 discordant, 528048 orphans, 11272 too large [>5000 bp], 23274644 duplicates)
Reads: 121499852 total, 66893 skipped (flags/unmapped)
Fragments: 60996712 total (60365584 tlen-paired, 5006 hash-paired, 469 singletons, 18037 discordant, 607616 orphans, 23810 too large [>5000 bp], 26235890 duplicates)
Reads: 123801092 total, 121911 skipped (flags/unmapped)
Fragments: 62379174 total (60698830 tlen-paired, 4317 hash-paired, 562 singletons, 333076 discordant, 1342389 orphans, 131892 too large [>5000 bp], 26702389 duplicates)