Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/da/e8306eb21dfdb0fda434802f3b0ab8/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_1CG-N1-BDNA-1_A23MHW3LT4_1/1136_1CG-N1-BDNA-1_A23MHW3LT4_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/da/e8306eb21dfdb0fda434802f3b0ab8/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_1CG-N1-BDNA-1_A23MHW3LT4_1/1136_1CG-N1-BDNA-1_A23MHW3LT4_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_1CG-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_1CG-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_1CG-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_1CG-N1-BDNA-1_A23MHW3LT4_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: 99738791 total, 63193 skipped (flags/unmapped)
Fragments: 50145175 total (49486486 tlen-paired, 3668 hash-paired, 637 singletons, 12449 discordant, 641935 orphans, 13910 too large [>5000 bp], 18105831 duplicates)
Reads: 95360963 total, 73736 skipped (flags/unmapped)
Fragments: 47947126 total (47290936 tlen-paired, 3537 hash-paired, 748 singletons, 18442 discordant, 633463 orphans, 13593 too large [>5000 bp], 17683873 duplicates)
Reads: 109296109 total, 70324 skipped (flags/unmapped)
Fragments: 54960340 total (54183978 tlen-paired, 7219 hash-paired, 621 singletons, 18892 discordant, 749630 orphans, 27678 too large [>5000 bp], 20312089 duplicates)
Reads: 111246989 total, 118027 skipped (flags/unmapped)
Fragments: 56244657 total (54111388 tlen-paired, 2735 hash-paired, 621 singletons, 417024 discordant, 1712889 orphans, 176579 too large [>5000 bp], 20623609 duplicates)