Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/659_epG-N1-BDNA-1_B23KGCJLT4_1/659_epG-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/659_epG-N1-BDNA-1_B23KGCJLT4_1/659_epG-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/9831af27cd732e93cf52734130220d/.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/8f/9831af27cd732e93cf52734130220d/.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] [W::hts_idx_load3] The index file is older than the data file: 659_epG-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.baiThe index file is older than the data file: 659_epG-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.baiThe index file is older than the data file: 659_epG-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai


[W::hts_idx_load3] The index file is older than the data file: 659_epG-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: 65608744 total, 34835 skipped (flags/unmapped)
Fragments: 32889875 total (32657458 tlen-paired, 1980 hash-paired, 338 singletons, 9418 discordant, 220681 orphans, 7589 too large [>5000 bp], 11470144 duplicates)
Reads: 60108345 total, 43169 skipped (flags/unmapped)
Fragments: 30129694 total (29897710 tlen-paired, 3615 hash-paired, 315 singletons, 13167 discordant, 214887 orphans, 10495 too large [>5000 bp], 10750349 duplicates)
Reads: 64815875 total, 36823 skipped (flags/unmapped)
Fragments: 32493270 total (32238328 tlen-paired, 3371 hash-paired, 236 singletons, 11563 discordant, 239772 orphans, 16260 too large [>5000 bp], 11675859 duplicates)
Reads: 71170783 total, 56523 skipped (flags/unmapped)
Fragments: 35746888 total (35157734 tlen-paired, 2869 hash-paired, 274 singletons, 112939 discordant, 473072 orphans, 46915 too large [>5000 bp], 12855568 duplicates)