Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/1101175d33b2d9e24ebba5718a8ffa/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_5P5-N1-BDNA-1_A23NMNVLT4_1/1136_5P5-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
  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/6c/1101175d33b2d9e24ebba5718a8ffa/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_5P5-N1-BDNA-1_A23NMNVLT4_1/1136_5P5-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
==> 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_5P5-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5P5-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5P5-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5P5-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: 88356770 total, 57213 skipped (flags/unmapped)
Fragments: 44265733 total (44000080 tlen-paired, 3333 hash-paired, 370 singletons, 11153 discordant, 250797 orphans, 9629 too large [>5000 bp], 11883489 duplicates)
Reads: 95513457 total, 50240 skipped (flags/unmapped)
Fragments: 47853584 total (47581604 tlen-paired, 3306 hash-paired, 438 singletons, 7979 discordant, 260257 orphans, 8372 too large [>5000 bp], 12723941 duplicates)
Reads: 104450853 total, 52232 skipped (flags/unmapped)
Fragments: 52337744 total (52008122 tlen-paired, 3725 hash-paired, 341 singletons, 11556 discordant, 314000 orphans, 18737 too large [>5000 bp], 14377308 duplicates)
Reads: 105339213 total, 89137 skipped (flags/unmapped)
Fragments: 52877542 total (52089902 tlen-paired, 4030 hash-paired, 419 singletons, 151032 discordant, 632159 orphans, 63785 too large [>5000 bp], 14530884 duplicates)