Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_BU9N-N1-BDNA-1_A23TY32LT4_1/1241_BU9N-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/279a7b587c4d5acda780462b889428/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_BU9N-N1-BDNA-1_A23TY32LT4_1/1241_BU9N-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
  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/ad/279a7b587c4d5acda780462b889428/.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_BU9N-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BU9N-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BU9N-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BU9N-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: 96724155 total, 58934 skipped (flags/unmapped)
Fragments: 48494948 total (48134758 tlen-paired, 3525 hash-paired, 433 singletons, 10530 discordant, 345702 orphans, 10730 too large [>5000 bp], 19930952 duplicates)
Reads: 89724742 total, 70116 skipped (flags/unmapped)
Fragments: 44977284 total (44629902 tlen-paired, 3890 hash-paired, 434 singletons, 15694 discordant, 327364 orphans, 13928 too large [>5000 bp], 18827106 duplicates)
Reads: 105828388 total, 65709 skipped (flags/unmapped)
Fragments: 53055464 total (52633622 tlen-paired, 6784 hash-paired, 356 singletons, 16165 discordant, 398537 orphans, 25322 too large [>5000 bp], 22295240 duplicates)
Reads: 107426097 total, 115269 skipped (flags/unmapped)
Fragments: 53982016 total (52962637 tlen-paired, 3417 hash-paired, 415 singletons, 198224 discordant, 817323 orphans, 82267 too large [>5000 bp], 22613900 duplicates)