Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_84Z-N1-BDNA-1_A23NMNVLT4_1/1136_84Z-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/8c225abae0be52157f4cf18a1a961a/.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/c7/8c225abae0be52157f4cf18a1a961a/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_84Z-N1-BDNA-1_A23NMNVLT4_1/1136_84Z-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
==> 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: 1136_84Z-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_84Z-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_84Z-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_84Z-N1-BDNA-1_A23NMNVLT4_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: 46991419 total, 37454 skipped (flags/unmapped)
Fragments: 23546146 total (23387405 tlen-paired, 1847 hash-paired, 225 singletons, 6899 discordant, 149770 orphans, 5834 too large [>5000 bp], 7237033 duplicates)
Reads: 50771702 total, 30594 skipped (flags/unmapped)
Fragments: 25444052 total (25281520 tlen-paired, 1630 hash-paired, 230 singletons, 4928 discordant, 155744 orphans, 4489 too large [>5000 bp], 7631090 duplicates)
Reads: 50771158 total, 32325 skipped (flags/unmapped)
Fragments: 25446516 total (25269295 tlen-paired, 2052 hash-paired, 165 singletons, 5730 discordant, 169274 orphans, 7620 too large [>5000 bp], 7858114 duplicates)
Reads: 56192181 total, 56399 skipped (flags/unmapped)
Fragments: 28213625 total (27751926 tlen-paired, 1544 hash-paired, 246 singletons, 91141 discordant, 368768 orphans, 38773 too large [>5000 bp], 8719847 duplicates)