Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/81a4770a5afd5972edfc622f7bd1ed/.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/48/81a4770a5afd5972edfc622f7bd1ed/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_LXR-N1-BDNA-1_B23MHTGLT4_1/1029_LXR-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_LXR-N1-BDNA-1_B23MHTGLT4_1/1029_LXR-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] The index file is older than the data file: 1029_LXR-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_LXR-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_LXR-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_LXR-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: 50057613 total, 38104 skipped (flags/unmapped)
Fragments: 25157594 total (24837551 tlen-paired, 2118 hash-paired, 265 singletons, 6732 discordant, 310928 orphans, 7757 too large [>5000 bp], 7848510 duplicates)
Reads: 52910455 total, 32634 skipped (flags/unmapped)
Fragments: 26597768 total (26247631 tlen-paired, 2251 hash-paired, 203 singletons, 5357 discordant, 342326 orphans, 12407 too large [>5000 bp], 8271584 duplicates)
Reads: 53485140 total, 30762 skipped (flags/unmapped)
Fragments: 26888899 total (26545745 tlen-paired, 1583 hash-paired, 321 singletons, 4999 discordant, 336251 orphans, 6576 too large [>5000 bp], 8129750 duplicates)
Reads: 59026953 total, 60806 skipped (flags/unmapped)
Fragments: 29832433 total (28727876 tlen-paired, 1467 hash-paired, 284 singletons, 224297 discordant, 878509 orphans, 90037 too large [>5000 bp], 9209700 duplicates)