Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1173_F0Y-N1-BDNA-01_B23MHTGLT4_1/1173_F0Y-N1-BDNA-01_B23MHTGLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/7edf90c4aee946c9adce654904bee3/.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/06/7edf90c4aee946c9adce654904bee3/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1173_F0Y-N1-BDNA-01_B23MHTGLT4_1/1173_F0Y-N1-BDNA-01_B23MHTGLT4_1.recalibrated.bam
==> 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: 1173_F0Y-N1-BDNA-01_B23MHTGLT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1173_F0Y-N1-BDNA-01_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y-N1-BDNA-01_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y-N1-BDNA-01_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: 66709362 total, 49986 skipped (flags/unmapped)
Fragments: 33477050 total (33150054 tlen-paired, 2963 hash-paired, 378 singletons, 13415 discordant, 310240 orphans, 7947 too large [>5000 bp], 10008126 duplicates)
Reads: 71110547 total, 42758 skipped (flags/unmapped)
Fragments: 35682828 total (35356330 tlen-paired, 2336 hash-paired, 383 singletons, 9269 discordant, 314510 orphans, 8513 too large [>5000 bp], 10462050 duplicates)
Reads: 70292120 total, 48645 skipped (flags/unmapped)
Fragments: 35273410 total (34920628 tlen-paired, 3566 hash-paired, 381 singletons, 11325 discordant, 337510 orphans, 17273 too large [>5000 bp], 10615879 duplicates)
Reads: 77886754 total, 78370 skipped (flags/unmapped)
Fragments: 39205182 total (38256750 tlen-paired, 2073 hash-paired, 432 singletons, 185183 discordant, 760744 orphans, 79598 too large [>5000 bp], 11801692 duplicates)