Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_01F-N1-BDNA-1_A23MHW3LT4_1/1136_01F-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/c78ad4a10933faa74cc5be02f5c3cc/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_01F-N1-BDNA-1_A23MHW3LT4_1/1136_01F-N1-BDNA-1_A23MHW3LT4_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/d6/c78ad4a10933faa74cc5be02f5c3cc/.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: 1136_01F-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_01F-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_01F-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_01F-N1-BDNA-1_A23MHW3LT4_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: 34405665 total, 46095 skipped (flags/unmapped)
Fragments: 17692120 total (16643958 tlen-paired, 4627 hash-paired, 295 singletons, 3129 discordant, 1040111 orphans, 7868 too large [>5000 bp], 8013070 duplicates)
Reads: 36095877 total, 46560 skipped (flags/unmapped)
Fragments: 18568926 total (17462842 tlen-paired, 3085 hash-paired, 369 singletons, 2502 discordant, 1100128 orphans, 5981 too large [>5000 bp], 8163096 duplicates)
Reads: 36364175 total, 43721 skipped (flags/unmapped)
Fragments: 18703607 total (17586787 tlen-paired, 5037 hash-paired, 260 singletons, 3003 discordant, 1108520 orphans, 11010 too large [>5000 bp], 8488996 duplicates)
Reads: 43990348 total, 74860 skipped (flags/unmapped)
Fragments: 23209844 total (19172119 tlen-paired, 2778 hash-paired, 390 singletons, 834283 discordant, 3200274 orphans, 348232 too large [>5000 bp], 9820760 duplicates)