Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_I9B-N1-BDNA-1_B23KGCJLT4_1/1029_I9B-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/e6bc470fd80d890c8f51ec1a961af4/.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/c6/e6bc470fd80d890c8f51ec1a961af4/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_I9B-N1-BDNA-1_B23KGCJLT4_1/1029_I9B-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: 1029_I9B-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1029_I9B-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_I9B-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_I9B-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: 65746563 total, 50145 skipped (flags/unmapped)
Fragments: 32946419 total (32711965 tlen-paired, 3867 hash-paired, 358 singletons, 12777 discordant, 217452 orphans, 10695 too large [>5000 bp], 11955407 duplicates)
Reads: 71138252 total, 38073 skipped (flags/unmapped)
Fragments: 35652315 total (35419467 tlen-paired, 2192 hash-paired, 339 singletons, 8665 discordant, 221652 orphans, 8770 too large [>5000 bp], 12655650 duplicates)
Reads: 77766449 total, 67871 skipped (flags/unmapped)
Fragments: 39049278 total (38435700 tlen-paired, 2280 hash-paired, 302 singletons, 115326 discordant, 495670 orphans, 47997 too large [>5000 bp], 14251860 duplicates)
Reads: 77873568 total, 45097 skipped (flags/unmapped)
Fragments: 39024850 total (38755760 tlen-paired, 3736 hash-paired, 276 singletons, 12843 discordant, 252235 orphans, 15641 too large [>5000 bp], 14237316 duplicates)