Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/07/bd2501f270bcd5e3b7560268257ff4/.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/07/bd2501f270bcd5e3b7560268257ff4/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_BW0I-N1-BDNA-1_A23TY32LT4_1/1241_BW0I-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_BW0I-N1-BDNA-1_A23TY32LT4_1/1241_BW0I-N1-BDNA-1_A23TY32LT4_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: 1241_BW0I-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1241_BW0I-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1241_BW0I-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1241_BW0I-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: 45483849 total, 35475 skipped (flags/unmapped)
Fragments: 22807963 total (22618338 tlen-paired, 2597 hash-paired, 248 singletons, 8262 discordant, 178518 orphans, 5607 too large [>5000 bp], 8728859 duplicates)
Reads: 48813250 total, 28617 skipped (flags/unmapped)
Fragments: 24480194 total (24286535 tlen-paired, 1488 hash-paired, 232 singletons, 5826 discordant, 186113 orphans, 5295 too large [>5000 bp], 9177679 duplicates)
Reads: 53618667 total, 31570 skipped (flags/unmapped)
Fragments: 26891010 total (26661464 tlen-paired, 2964 hash-paired, 174 singletons, 8757 discordant, 217651 orphans, 11451 too large [>5000 bp], 10294243 duplicates)
Reads: 54166772 total, 56210 skipped (flags/unmapped)
Fragments: 27233934 total (26682545 tlen-paired, 2606 hash-paired, 236 singletons, 105917 discordant, 442630 orphans, 42780 too large [>5000 bp], 10421070 duplicates)