Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1029_BCL1-N1-BDNA-1_A23NMNVLT4_1/1029_BCL1-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1029_BCL1-N1-BDNA-1_A23NMNVLT4_1/1029_BCL1-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d0/892971f6e7d6d9f705598ebecb0931/.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/d0/892971f6e7d6d9f705598ebecb0931/.command.run
==> 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: 1029_BCL1-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BCL1-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1029_BCL1-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BCL1-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: 73059528 total, 46726 skipped (flags/unmapped)
Fragments: 36603041 total (36378629 tlen-paired, 2554 hash-paired, 359 singletons, 11248 discordant, 210251 orphans, 8665 too large [>5000 bp], 8584263 duplicates)
Reads: 78908998 total, 37663 skipped (flags/unmapped)
Fragments: 39536339 total (39310817 tlen-paired, 2633 hash-paired, 317 singletons, 7824 discordant, 214748 orphans, 6861 too large [>5000 bp], 9152949 duplicates)
Reads: 85304271 total, 42222 skipped (flags/unmapped)
Fragments: 42743396 total (42477477 tlen-paired, 5217 hash-paired, 285 singletons, 11847 discordant, 248570 orphans, 12056 too large [>5000 bp], 10237080 duplicates)
Reads: 86158317 total, 67733 skipped (flags/unmapped)
Fragments: 43244634 total (42631135 tlen-paired, 2591 hash-paired, 383 singletons, 116684 discordant, 493841 orphans, 47770 too large [>5000 bp], 10352045 duplicates)