Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1047_LM-N1-BDNA-1_B23MHTGLT4_1/1047_LM-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/af52db7c418c70fe9faef25ff417fb/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1047_LM-N1-BDNA-1_B23MHTGLT4_1/1047_LM-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam
  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/2d/af52db7c418c70fe9faef25ff417fb/.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: 1047_LM-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_LM-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_LM-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_LM-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: 87823126 total, 64414 skipped (flags/unmapped)
Fragments: 44094559 total (43629711 tlen-paired, 3774 hash-paired, 611 singletons, 15048 discordant, 445415 orphans, 7810 too large [>5000 bp], 13795702 duplicates)
Reads: 93069937 total, 54478 skipped (flags/unmapped)
Fragments: 46726288 total (46258290 tlen-paired, 3053 hash-paired, 611 singletons, 10100 discordant, 454234 orphans, 8864 too large [>5000 bp], 14332461 duplicates)
Reads: 101746449 total, 61886 skipped (flags/unmapped)
Fragments: 51085083 total (50533171 tlen-paired, 4335 hash-paired, 506 singletons, 15652 discordant, 531419 orphans, 23161 too large [>5000 bp], 16132090 duplicates)
Reads: 103436995 total, 95855 skipped (flags/unmapped)
Fragments: 52141309 total (50665047 tlen-paired, 3698 hash-paired, 587 singletons, 287778 discordant, 1184199 orphans, 121654 too large [>5000 bp], 16429320 duplicates)