Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/6ee47c1601dca6f481cf2d414dbc7d/.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/54/6ee47c1601dca6f481cf2d414dbc7d/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_BD47-N1-BDNA-1_B23MHTGLT4_1/1029_BD47-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_BD47-N1-BDNA-1_B23MHTGLT4_1/1029_BD47-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_BD47-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1029_BD47-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BD47-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BD47-N1-BDNA-1_B23MHTGLT4_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: 94406841 total, 69375 skipped (flags/unmapped)
Fragments: 47357843 total (46936477 tlen-paired, 4469 hash-paired, 485 singletons, 14043 discordant, 402369 orphans, 12317 too large [>5000 bp], 14210609 duplicates)
Reads: 99332534 total, 61068 skipped (flags/unmapped)
Fragments: 49837495 total (49378886 tlen-paired, 4042 hash-paired, 488 singletons, 12333 discordant, 441746 orphans, 19355 too large [>5000 bp], 15080381 duplicates)
Reads: 101369645 total, 60073 skipped (flags/unmapped)
Fragments: 50852220 total (50419593 tlen-paired, 4057 hash-paired, 497 singletons, 10322 discordant, 417751 orphans, 11690 too large [>5000 bp], 14942449 duplicates)
Reads: 109962245 total, 102347 skipped (flags/unmapped)
Fragments: 55335992 total (54043536 tlen-paired, 3193 hash-paired, 569 singletons, 256199 discordant, 1032495 orphans, 110489 too large [>5000 bp], 16730240 duplicates)