Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/7a344cae51b79311bfd7bdda00f2cb/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1029_DPZ-N1-BDNA-1_B23KFG5LT4_1/1029_DPZ-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
  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/5f/7a344cae51b79311bfd7bdda00f2cb/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1029_DPZ-N1-BDNA-1_B23KFG5LT4_1/1029_DPZ-N1-BDNA-1_B23KFG5LT4_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_DPZ-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_DPZ-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_DPZ-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_DPZ-N1-BDNA-1_B23KFG5LT4_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: 94652540 total, 56400 skipped (flags/unmapped)
Fragments: 47453400 total (47101528 tlen-paired, 3278 hash-paired, 493 singletons, 12270 discordant, 335831 orphans, 12832 too large [>5000 bp], 19680060 duplicates)
Reads: 90150730 total, 69634 skipped (flags/unmapped)
Fragments: 45192157 total (44836902 tlen-paired, 3654 hash-paired, 435 singletons, 18993 discordant, 332173 orphans, 14695 too large [>5000 bp], 19142960 duplicates)
Reads: 105360362 total, 61259 skipped (flags/unmapped)
Fragments: 52827485 total (52415431 tlen-paired, 3595 hash-paired, 372 singletons, 18548 discordant, 389539 orphans, 17022 too large [>5000 bp], 22405959 duplicates)
Reads: 106417084 total, 101654 skipped (flags/unmapped)
Fragments: 53468603 total (52513413 tlen-paired, 4406 hash-paired, 419 singletons, 180120 discordant, 770245 orphans, 74444 too large [>5000 bp], 22659440 duplicates)