Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1136_6FA-N1-BDNA-1_B23MHTGLT4_1/1136_6FA-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/2b32c635b209913037eedc36495ef1/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/2b32c635b209913037eedc36495ef1/.command.run
  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-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1136_6FA-N1-BDNA-1_B23MHTGLT4_1/1136_6FA-N1-BDNA-1_B23MHTGLT4_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_6FA-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6FA-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6FA-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_6FA-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: 78112330 total, 56186 skipped (flags/unmapped)
Fragments: 39237979 total (38781690 tlen-paired, 3009 hash-paired, 430 singletons, 13326 discordant, 439524 orphans, 10070 too large [>5000 bp], 14391207 duplicates)
Reads: 82076903 total, 46577 skipped (flags/unmapped)
Fragments: 41232662 total (40767763 tlen-paired, 2568 hash-paired, 427 singletons, 8773 discordant, 453131 orphans, 9280 too large [>5000 bp], 14768825 duplicates)
Reads: 90250895 total, 52324 skipped (flags/unmapped)
Fragments: 45342420 total (44800101 tlen-paired, 5025 hash-paired, 396 singletons, 13631 discordant, 523267 orphans, 18697 too large [>5000 bp], 16638148 duplicates)
Reads: 91646809 total, 84146 skipped (flags/unmapped)
Fragments: 46258574 total (44768107 tlen-paired, 2253 hash-paired, 413 singletons, 291899 discordant, 1195902 orphans, 120915 too large [>5000 bp], 16924657 duplicates)