Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_3LE-N1-BDNA-1_A23TY32LT4_1/1241_3LE-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/a310f28423c688d6c8051259dc48f0/.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/c1/a310f28423c688d6c8051259dc48f0/.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_3LE-N1-BDNA-1_A23TY32LT4_1/1241_3LE-N1-BDNA-1_A23TY32LT4_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: 1241_3LE-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_3LE-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1241_3LE-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_3LE-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: 69265402 total, 48526 skipped (flags/unmapped)
Fragments: 34716275 total (34472472 tlen-paired, 3316 hash-paired, 367 singletons, 10995 discordant, 229125 orphans, 6909 too large [>5000 bp], 12439466 duplicates)
Reads: 75945112 total, 43170 skipped (flags/unmapped)
Fragments: 38064096 total (37809565 tlen-paired, 2799 hash-paired, 297 singletons, 7380 discordant, 244055 orphans, 9051 too large [>5000 bp], 13390269 duplicates)
Reads: 82856514 total, 86176 skipped (flags/unmapped)
Fragments: 41613039 total (40899873 tlen-paired, 4670 hash-paired, 269 singletons, 136896 discordant, 571331 orphans, 57930 too large [>5000 bp], 14984997 duplicates)
Reads: 81947627 total, 46081 skipped (flags/unmapped)
Fragments: 41075470 total (40772884 tlen-paired, 3913 hash-paired, 252 singletons, 11591 discordant, 286830 orphans, 18844 too large [>5000 bp], 14785571 duplicates)