Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/659_8h-N1-BDNA-1_B23KGCJLT4_1/659_8h-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/0a81f81d3228937b58de3b8bf9e7a7/.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/9e/0a81f81d3228937b58de3b8bf9e7a7/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/659_8h-N1-BDNA-1_B23KGCJLT4_1/659_8h-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
==> 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: 659_8h-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.baiThe index file is older than the data file: 659_8h-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 659_8h-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_8h-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
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 69447660 total, 51760 skipped (flags/unmapped)
Fragments: 34812736 total (34538918 tlen-paired, 3196 hash-paired, 351 singletons, 18288 discordant, 251983 orphans, 11381 too large [>5000 bp], 13293227 duplicates)
Reads: 75369511 total, 42727 skipped (flags/unmapped)
Fragments: 37778305 total (37510251 tlen-paired, 3052 hash-paired, 369 singletons, 13128 discordant, 251505 orphans, 11024 too large [>5000 bp], 14128339 duplicates)
Reads: 82050242 total, 73485 skipped (flags/unmapped)
Fragments: 41193030 total (40566832 tlen-paired, 2478 hash-paired, 298 singletons, 116579 discordant, 506843 orphans, 48919 too large [>5000 bp], 15914512 duplicates)
Reads: 74952099 total, 47046 skipped (flags/unmapped)
Fragments: 37577470 total (37268893 tlen-paired, 4710 hash-paired, 286 singletons, 15856 discordant, 287725 orphans, 19062 too large [>5000 bp], 14479575 duplicates)