Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_JAD-N1-BDNA-1_B23MHTGLT4_1/1029_JAD-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_JAD-N1-BDNA-1_B23MHTGLT4_1/1029_JAD-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/c7e51fd9f5abb2ace2625691eaaafc/.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/fb/c7e51fd9f5abb2ace2625691eaaafc/.command.run
==> 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: 1029_JAD-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_JAD-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_JAD-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_JAD-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: 88124469 total, 68817 skipped (flags/unmapped)
Fragments: 44236861 total (43773866 tlen-paired, 5220 hash-paired, 432 singletons, 16553 discordant, 440790 orphans, 11576 too large [>5000 bp], 13995689 duplicates)
Reads: 93554705 total, 53587 skipped (flags/unmapped)
Fragments: 46964440 total (46501390 tlen-paired, 3998 hash-paired, 597 singletons, 10706 discordant, 447749 orphans, 10292 too large [>5000 bp], 14647852 duplicates)
Reads: 101982127 total, 59797 skipped (flags/unmapped)
Fragments: 51201580 total (50658001 tlen-paired, 4049 hash-paired, 428 singletons, 16534 discordant, 522568 orphans, 21083 too large [>5000 bp], 16312684 duplicates)
Reads: 103184667 total, 94492 skipped (flags/unmapped)
Fragments: 52002394 total (50578811 tlen-paired, 4003 hash-paired, 516 singletons, 274871 discordant, 1144193 orphans, 115048 too large [>5000 bp], 16554701 duplicates)