Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_253-N1-BDNA-1_B23KGCJLT4_1/1136_253-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_253-N1-BDNA-1_B23KGCJLT4_1/1136_253-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/c7b58146fa44a72485ad8aeba0f9be/.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/41/c7b58146fa44a72485ad8aeba0f9be/.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_253-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_253-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_253-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_253-N1-BDNA-1_B23KGCJLT4_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
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Loaded 472416 probes across 3366 contigs
Reads: 88178755 total, 58853 skipped (flags/unmapped)
Fragments: 44165093 total (43913442 tlen-paired, 3844 hash-paired, 363 singletons, 14603 discordant, 232841 orphans, 11460 too large [>5000 bp], 15787098 duplicates)
Reads: 94231165 total, 54992 skipped (flags/unmapped)
Fragments: 47202248 total (46897895 tlen-paired, 5138 hash-paired, 341 singletons, 12936 discordant, 285938 orphans, 28978 too large [>5000 bp], 17006822 duplicates)
Reads: 95211053 total, 48494 skipped (flags/unmapped)
Fragments: 47688120 total (47441650 tlen-paired, 2515 hash-paired, 457 singletons, 10466 discordant, 233032 orphans, 9904 too large [>5000 bp], 16746274 duplicates)
Reads: 104199759 total, 82946 skipped (flags/unmapped)
Fragments: 52252588 total (51642167 tlen-paired, 3486 hash-paired, 375 singletons, 115572 discordant, 490988 orphans, 51500 too large [>5000 bp], 18891700 duplicates)