Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_RJ7-N1-BDNA-1_B23MHTGLT4_1/1029_RJ7-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_RJ7-N1-BDNA-1_B23MHTGLT4_1/1029_RJ7-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/bcd3dcaf36acebe8001103d8b59bc3/.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/54/bcd3dcaf36acebe8001103d8b59bc3/.command.run
==> 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_RJ7-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_RJ7-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_RJ7-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_RJ7-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: 68053608 total, 56687 skipped (flags/unmapped)
Fragments: 34255282 total (33708590 tlen-paired, 2559 hash-paired, 452 singletons, 10848 discordant, 532833 orphans, 9821 too large [>5000 bp], 12065493 duplicates)
Reads: 71677471 total, 51409 skipped (flags/unmapped)
Fragments: 36083745 total (35511492 tlen-paired, 2621 hash-paired, 511 singletons, 8016 discordant, 561105 orphans, 10094 too large [>5000 bp], 12356457 duplicates)
Reads: 78311200 total, 51484 skipped (flags/unmapped)
Fragments: 39422821 total (38791726 tlen-paired, 2416 hash-paired, 377 singletons, 11141 discordant, 617161 orphans, 15806 too large [>5000 bp], 13862595 duplicates)
Reads: 80368855 total, 94026 skipped (flags/unmapped)
Fragments: 40749587 total (38826294 tlen-paired, 2574 hash-paired, 500 singletons, 381900 discordant, 1538319 orphans, 157237 too large [>5000 bp], 14144083 duplicates)