Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_NID-N1-BDNA-1_A23TY32LT4_1/1241_NID-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_NID-N1-BDNA-1_A23TY32LT4_1/1241_NID-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/82/22affb673d5c056902106d9c8fd087/.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/82/22affb673d5c056902106d9c8fd087/.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: 1241_NID-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_NID-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_NID-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_NID-N1-BDNA-1_A23TY32LT4_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: 95897086 total, 69197 skipped (flags/unmapped)
Fragments: 48068758 total (47711309 tlen-paired, 4943 hash-paired, 419 singletons, 15899 discordant, 336188 orphans, 13490 too large [>5000 bp], 20034850 duplicates)
Reads: 103026193 total, 58904 skipped (flags/unmapped)
Fragments: 51649048 total (51280532 tlen-paired, 3677 hash-paired, 411 singletons, 10900 discordant, 353528 orphans, 11566 too large [>5000 bp], 21224779 duplicates)
Reads: 113045386 total, 63444 skipped (flags/unmapped)
Fragments: 56674802 total (56243438 tlen-paired, 4947 hash-paired, 362 singletons, 16091 discordant, 409964 orphans, 21332 too large [>5000 bp], 23837220 duplicates)
Reads: 114764111 total, 113188 skipped (flags/unmapped)
Fragments: 57661579 total (56616627 tlen-paired, 3654 hash-paired, 408 singletons, 203553 discordant, 837337 orphans, 82755 too large [>5000 bp], 24204039 duplicates)