Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_BSJ7-N1-BDNA-1_A23KFG7LT4_1/1029_BSJ7-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/55bb7c92dffe25e68df40f9de8b81e/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_BSJ7-N1-BDNA-1_A23KFG7LT4_1/1029_BSJ7-N1-BDNA-1_A23KFG7LT4_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/fc/55bb7c92dffe25e68df40f9de8b81e/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_BSJ7-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BSJ7-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_BSJ7-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BSJ7-N1-BDNA-1_A23KFG7LT4_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: 74920316 total, 53647 skipped (flags/unmapped)
Fragments: 37664686 total (37160413 tlen-paired, 3242 hash-paired, 424 singletons, 15186 discordant, 485421 orphans, 11571 too large [>5000 bp], 14419532 duplicates)
Reads: 79914721 total, 45922 skipped (flags/unmapped)
Fragments: 40176513 total (39659189 tlen-paired, 2876 hash-paired, 461 singletons, 10523 discordant, 503464 orphans, 9849 too large [>5000 bp], 14941149 duplicates)
Reads: 86921018 total, 49502 skipped (flags/unmapped)
Fragments: 43704805 total (43105315 tlen-paired, 3752 hash-paired, 357 singletons, 15936 discordant, 579445 orphans, 20854 too large [>5000 bp], 16718769 duplicates)
Reads: 89659317 total, 80152 skipped (flags/unmapped)
Fragments: 45314307 total (43665510 tlen-paired, 2828 hash-paired, 413 singletons, 327404 discordant, 1318152 orphans, 134558 too large [>5000 bp], 17253580 duplicates)