Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_BDX8-N1-BDNA-1_B23L5TMLT4_1/1029_BDX8-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/4a98be77cc4ea7e7595e4683a795d0/.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/cd/4a98be77cc4ea7e7595e4683a795d0/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_BDX8-N1-BDNA-1_B23L5TMLT4_1/1029_BDX8-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
==> 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_BDX8-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_BDX8-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_BDX8-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BDX8-N1-BDNA-1_B23L5TMLT4_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: 62495362 total, 51630 skipped (flags/unmapped)
Fragments: 31350202 total (31061230 tlen-paired, 3410 hash-paired, 398 singletons, 10556 discordant, 274608 orphans, 9167 too large [>5000 bp], 11056358 duplicates)
Reads: 67349162 total, 42346 skipped (flags/unmapped)
Fragments: 33787779 total (33491722 tlen-paired, 2772 hash-paired, 428 singletons, 7373 discordant, 285484 orphans, 8585 too large [>5000 bp], 11695831 duplicates)
Reads: 73100726 total, 47110 skipped (flags/unmapped)
Fragments: 36672359 total (36321668 tlen-paired, 4540 hash-paired, 380 singletons, 11017 discordant, 334754 orphans, 22016 too large [>5000 bp], 12960704 duplicates)
Reads: 73806945 total, 81290 skipped (flags/unmapped)
Fragments: 37146345 total (36261261 tlen-paired, 3166 hash-paired, 401 singletons, 171103 discordant, 710414 orphans, 71890 too large [>5000 bp], 13070746 duplicates)