Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/0422661fd006f4f4d9b75752b89db6/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_87H-N1-BDNA-1_B23KFG5LT4_1/1136_87H-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/b8/0422661fd006f4f4d9b75752b89db6/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_87H-N1-BDNA-1_B23KFG5LT4_1/1136_87H-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_87H-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_87H-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_87H-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_87H-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: 72717362 total, 45036 skipped (flags/unmapped)
Fragments: 36455709 total (36187382 tlen-paired, 2191 hash-paired, 377 singletons, 9068 discordant, 256691 orphans, 8988 too large [>5000 bp], 14266596 duplicates)
Reads: 68375577 total, 55118 skipped (flags/unmapped)
Fragments: 34273864 total (34007781 tlen-paired, 2451 hash-paired, 428 singletons, 13713 discordant, 249491 orphans, 11325 too large [>5000 bp], 13708711 duplicates)
Reads: 80505632 total, 80089 skipped (flags/unmapped)
Fragments: 40449871 total (39722664 tlen-paired, 1632 hash-paired, 329 singletons, 137908 discordant, 587338 orphans, 56734 too large [>5000 bp], 16272528 duplicates)
Reads: 80525970 total, 50721 skipped (flags/unmapped)
Fragments: 40369259 total (40062272 tlen-paired, 4442 hash-paired, 300 singletons, 13240 discordant, 289005 orphans, 13018 too large [>5000 bp], 16224625 duplicates)