Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/9b8d0460b20ba15d3c73cedf53283b/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_5NN-N1-BDNA-1_B23KFG5LT4_1/1136_5NN-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
  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/3c/9b8d0460b20ba15d3c73cedf53283b/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_5NN-N1-BDNA-1_B23KFG5LT4_1/1136_5NN-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_5NN-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5NN-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5NN-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5NN-N1-BDNA-1_B23KFG5LT4_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: 83478184 total, 66952 skipped (flags/unmapped)
Fragments: 41885224 total (41476463 tlen-paired, 3378 hash-paired, 344 singletons, 17481 discordant, 387558 orphans, 14343 too large [>5000 bp], 19034705 duplicates)
Reads: 88209400 total, 55961 skipped (flags/unmapped)
Fragments: 44267366 total (43848001 tlen-paired, 2147 hash-paired, 490 singletons, 12179 discordant, 404549 orphans, 11873 too large [>5000 bp], 19583976 duplicates)
Reads: 98593933 total, 97531 skipped (flags/unmapped)
Fragments: 49639316 total (48430414 tlen-paired, 3535 hash-paired, 430 singletons, 233349 discordant, 971588 orphans, 94894 too large [>5000 bp], 22484783 duplicates)
Reads: 97309273 total, 63578 skipped (flags/unmapped)
Fragments: 48832596 total (48326120 tlen-paired, 3354 hash-paired, 277 singletons, 17837 discordant, 485008 orphans, 32894 too large [>5000 bp], 22167641 duplicates)