Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/b9d7946eef04d420e9cdd2c9c7a907/.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/b0/b9d7946eef04d420e9cdd2c9c7a907/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/869_FH7-N1-BDNA-1_A23H3NYLT3_1/869_FH7-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/869_FH7-N1-BDNA-1_A23H3NYLT3_1/869_FH7-N1-BDNA-1_A23H3NYLT3_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: 869_FH7-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_FH7-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_FH7-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_FH7-N1-BDNA-1_A23H3NYLT3_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: 76209421 total, 67086 skipped (flags/unmapped)
Fragments: 38249223 total (37850030 tlen-paired, 20940 hash-paired, 7949 singletons, 7964 discordant, 362340 orphans, 7089 too large [>5000 bp], 5297982 duplicates)
Reads: 83080797 total, 62039 skipped (flags/unmapped)
Fragments: 41710332 total (41253953 tlen-paired, 22226 hash-paired, 8603 singletons, 6349 discordant, 419201 orphans, 12949 too large [>5000 bp], 5767296 duplicates)
Reads: 82359431 total, 64025 skipped (flags/unmapped)
Fragments: 41345080 total (40891636 tlen-paired, 24848 hash-paired, 8492 singletons, 8172 discordant, 411932 orphans, 12835 too large [>5000 bp], 5703735 duplicates)
Reads: 83532635 total, 95110 skipped (flags/unmapped)
Fragments: 42150418 total (40818381 tlen-paired, 20613 hash-paired, 8338 singletons, 253661 discordant, 1049425 orphans, 97226 too large [>5000 bp], 5758548 duplicates)