Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_1QV-N1-BDNA-1_A23MHW3LT4_1/1136_1QV-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/5bae2b0de73986e59709f28162226c/.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/b0/5bae2b0de73986e59709f28162226c/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_1QV-N1-BDNA-1_A23MHW3LT4_1/1136_1QV-N1-BDNA-1_A23MHW3LT4_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_1QV-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_1QV-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_1QV-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_1QV-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: 81707404 total, 60812 skipped (flags/unmapped)
Fragments: 41034766 total (40561016 tlen-paired, 4200 hash-paired, 535 singletons, 19518 discordant, 449497 orphans, 13546 too large [>5000 bp], 13864203 duplicates)
Reads: 87172948 total, 51288 skipped (flags/unmapped)
Fragments: 43777889 total (43305668 tlen-paired, 3131 hash-paired, 528 singletons, 12816 discordant, 455746 orphans, 11078 too large [>5000 bp], 14449007 duplicates)
Reads: 95224146 total, 54345 skipped (flags/unmapped)
Fragments: 47826582 total (47280505 tlen-paired, 4911 hash-paired, 474 singletons, 19639 discordant, 521053 orphans, 19082 too large [>5000 bp], 16218446 duplicates)
Reads: 96133782 total, 86033 skipped (flags/unmapped)
Fragments: 48477318 total (47072750 tlen-paired, 2083 hash-paired, 529 singletons, 270536 discordant, 1131420 orphans, 112531 too large [>5000 bp], 16442409 duplicates)