Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_04H-N1-BDNA-1_A23MHW3LT4_1/1136_04H-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/28d9255f669c64516300770341b6f7/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_04H-N1-BDNA-1_A23MHW3LT4_1/1136_04H-N1-BDNA-1_A23MHW3LT4_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/e9/28d9255f669c64516300770341b6f7/.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: 1136_04H-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_04H-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_04H-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_04H-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: 77096461 total, 63843 skipped (flags/unmapped)
Fragments: 38751896 total (38236259 tlen-paired, 3665 hash-paired, 398 singletons, 14832 discordant, 496742 orphans, 12983 too large [>5000 bp], 14414467 duplicates)
Reads: 81394689 total, 53939 skipped (flags/unmapped)
Fragments: 40916966 total (40390267 tlen-paired, 2919 hash-paired, 497 singletons, 9910 discordant, 513373 orphans, 10344 too large [>5000 bp], 14865409 duplicates)
Reads: 90526878 total, 98970 skipped (flags/unmapped)
Fragments: 45755210 total (44055715 tlen-paired, 4421 hash-paired, 435 singletons, 331466 discordant, 1363173 orphans, 140548 too large [>5000 bp], 16932333 duplicates)
Reads: 90469208 total, 59429 skipped (flags/unmapped)
Fragments: 45485522 total (44858810 tlen-paired, 6362 hash-paired, 479 singletons, 15303 discordant, 604568 orphans, 21891 too large [>5000 bp], 16939989 duplicates)