Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_BCZQ-N1-BDNA-1_B23H2GYLT3_1/1029_BCZQ-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/be11b0ba28fd5a6f291d302ba23cfa/.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/d1/be11b0ba28fd5a6f291d302ba23cfa/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_BCZQ-N1-BDNA-1_B23H2GYLT3_1/1029_BCZQ-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_BCZQ-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai[W::hts_idx_load3] The index file is older than the data file: 1029_BCZQ-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai

Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_BCZQ-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BCZQ-N1-BDNA-1_B23H2GYLT3_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: 89538134 total, 76098 skipped (flags/unmapped)
Fragments: 44931458 total (44483332 tlen-paired, 17846 hash-paired, 7040 singletons, 8794 discordant, 414446 orphans, 10303 too large [>5000 bp], 10203126 duplicates)
Reads: 97758179 total, 63655 skipped (flags/unmapped)
Fragments: 49078561 total (48572402 tlen-paired, 18188 hash-paired, 7364 singletons, 6479 discordant, 474128 orphans, 9447 too large [>5000 bp], 11060616 duplicates)
Reads: 98116502 total, 66697 skipped (flags/unmapped)
Fragments: 49253132 total (48745680 tlen-paired, 17886 hash-paired, 7478 singletons, 8755 discordant, 473333 orphans, 12176 too large [>5000 bp], 11105286 duplicates)
Reads: 100058920 total, 109478 skipped (flags/unmapped)
Fragments: 50472080 total (48934001 tlen-paired, 19747 hash-paired, 7508 singletons, 294258 discordant, 1216566 orphans, 114678 too large [>5000 bp], 11296030 duplicates)