Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/7acd275d2aaeb310334eb4263ffce5/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_BJND-N1-BDNA-1_B23MHTGLT4_1/1029_BJND-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_BJND-N1-BDNA-1_B23MHTGLT4_1/1029_BJND-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
  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/4c/7acd275d2aaeb310334eb4263ffce5/.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_BJND-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1029_BJND-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BJND-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BJND-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: 81068500 total, 58973 skipped (flags/unmapped)
Fragments: 40725366 total (40250597 tlen-paired, 3540 hash-paired, 382 singletons, 12280 discordant, 458567 orphans, 8872 too large [>5000 bp], 12987097 duplicates)
Reads: 85986245 total, 51004 skipped (flags/unmapped)
Fragments: 43195314 total (42710517 tlen-paired, 2580 hash-paired, 500 singletons, 8408 discordant, 473309 orphans, 9211 too large [>5000 bp], 13535678 duplicates)
Reads: 94091843 total, 54237 skipped (flags/unmapped)
Fragments: 47274621 total (46712189 tlen-paired, 6135 hash-paired, 418 singletons, 12245 discordant, 543634 orphans, 16208 too large [>5000 bp], 15154855 duplicates)
Reads: 95711255 total, 86686 skipped (flags/unmapped)
Fragments: 48321655 total (46725725 tlen-paired, 2425 hash-paired, 536 singletons, 313934 discordant, 1279035 orphans, 130415 too large [>5000 bp], 15444582 duplicates)