Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/659_dhS-N1-BDNA-1_B23MHTGLT4_1/659_dhS-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/d1c5842cde839e1a47db43aba1e6a8/.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/81/d1c5842cde839e1a47db43aba1e6a8/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/659_dhS-N1-BDNA-1_B23MHTGLT4_1/659_dhS-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 659_dhS-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
The index file is older than the data file: 659_dhS-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_dhS-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_dhS-N1-BDNA-1_B23MHTGLT4_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: 34646510 total, 26534 skipped (flags/unmapped)
Fragments: 17408482 total (17195427 tlen-paired, 1345 hash-paired, 201 singletons, 6852 discordant, 204657 orphans, 3935 too large [>5000 bp], 5123710 duplicates)
Reads: 37196686 total, 22661 skipped (flags/unmapped)
Fragments: 18689006 total (18469839 tlen-paired, 1387 hash-paired, 268 singletons, 4835 discordant, 212677 orphans, 4479 too large [>5000 bp], 5393850 duplicates)
Reads: 40428709 total, 26067 skipped (flags/unmapped)
Fragments: 20314274 total (20064575 tlen-paired, 2213 hash-paired, 195 singletons, 7150 discordant, 240141 orphans, 7215 too large [>5000 bp], 6018080 duplicates)
Reads: 40899936 total, 41409 skipped (flags/unmapped)
Fragments: 20650428 total (19963317 tlen-paired, 1489 hash-paired, 216 singletons, 133881 discordant, 551525 orphans, 54706 too large [>5000 bp], 6102913 duplicates)