Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/1c6c1a70fb1b459fce43dba2a310be/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/659_drH-N1-BDNA-1_B23MHTGLT4_1/659_drH-N1-BDNA-1_B23MHTGLT4_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/c9/1c6c1a70fb1b459fce43dba2a310be/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/659_drH-N1-BDNA-1_B23MHTGLT4_1/659_drH-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
==> 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: 659_drH-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_drH-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 659_drH-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_drH-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
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 63822210 total, 47804 skipped (flags/unmapped)
Fragments: 32040593 total (31703542 tlen-paired, 2795 hash-paired, 341 singletons, 11042 discordant, 322873 orphans, 8217 too large [>5000 bp], 9072740 duplicates)
Reads: 67738810 total, 40916 skipped (flags/unmapped)
Fragments: 34005903 total (33666184 tlen-paired, 2681 hash-paired, 400 singletons, 7502 discordant, 329136 orphans, 7812 too large [>5000 bp], 9440939 duplicates)
Reads: 74765525 total, 70695 skipped (flags/unmapped)
Fragments: 37687940 total (36621172 tlen-paired, 2159 hash-paired, 413 singletons, 207199 discordant, 856997 orphans, 88180 too large [>5000 bp], 10718581 duplicates)
Reads: 73895730 total, 45052 skipped (flags/unmapped)
Fragments: 37103273 total (36697353 tlen-paired, 3723 hash-paired, 354 singletons, 11259 discordant, 390584 orphans, 17535 too large [>5000 bp], 10556563 duplicates)