Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_86S-N1-BDNA-1_B23KGCJLT4_1/1136_86S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_86S-N1-BDNA-1_B23KGCJLT4_1/1136_86S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/1ea6fe26e962dcc1c675a585614793/.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/4e/1ea6fe26e962dcc1c675a585614793/.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: 1136_86S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_86S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_86S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_86S-N1-BDNA-1_B23KGCJLT4_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: 82980653 total, 57306 skipped (flags/unmapped)
Fragments: 41588841 total (41293484 tlen-paired, 3639 hash-paired, 430 singletons, 15607 discordant, 275681 orphans, 10888 too large [>5000 bp], 16863621 duplicates)
Reads: 88989461 total, 48147 skipped (flags/unmapped)
Fragments: 44599199 total (44306387 tlen-paired, 3146 hash-paired, 466 singletons, 11326 discordant, 277874 orphans, 10628 too large [>5000 bp], 17725554 duplicates)
Reads: 89115305 total, 51709 skipped (flags/unmapped)
Fragments: 44668834 total (44316852 tlen-paired, 5679 hash-paired, 349 singletons, 14253 discordant, 331701 orphans, 28989 too large [>5000 bp], 18192388 duplicates)
Reads: 98515349 total, 79724 skipped (flags/unmapped)
Fragments: 49460494 total (48701234 tlen-paired, 2688 hash-paired, 328 singletons, 146609 discordant, 609635 orphans, 62300 too large [>5000 bp], 20158592 duplicates)