Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/659_doL-N1-BDNA-1_A23TY32LT4_1/659_doL-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/864a54c3faf9d6983c0bc5f9452c20/.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/bd/864a54c3faf9d6983c0bc5f9452c20/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/659_doL-N1-BDNA-1_A23TY32LT4_1/659_doL-N1-BDNA-1_A23TY32LT4_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: 659_doL-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_doL-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
The index file is older than the data file: 659_doL-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_doL-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: 86659985 total, 64215 skipped (flags/unmapped)
Fragments: 43430855 total (43122095 tlen-paired, 5340 hash-paired, 284 singletons, 14350 discordant, 288786 orphans, 11565 too large [>5000 bp], 16571372 duplicates)
Reads: 93797300 total, 52970 skipped (flags/unmapped)
Fragments: 47014930 total (46673285 tlen-paired, 4410 hash-paired, 286 singletons, 12549 discordant, 324400 orphans, 19578 too large [>5000 bp], 18132890 duplicates)
Reads: 94890281 total, 50132 skipped (flags/unmapped)
Fragments: 47563810 total (47243488 tlen-paired, 3874 hash-paired, 399 singletons, 10389 discordant, 305660 orphans, 9294 too large [>5000 bp], 17958059 duplicates)
Reads: 103654821 total, 97750 skipped (flags/unmapped)
Fragments: 52055127 total (51185538 tlen-paired, 4182 hash-paired, 321 singletons, 171376 discordant, 693710 orphans, 70424 too large [>5000 bp], 20086391 duplicates)