Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BJHR-N1-BDNA-1_A23TNVNLT4_1/1241_BJHR-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/02bc9635c076a1f9793a203ffbc06b/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BJHR-N1-BDNA-1_A23TNVNLT4_1/1241_BJHR-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  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/89/02bc9635c076a1f9793a203ffbc06b/.command.run
==> 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: 1241_BJHR-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BJHR-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BJHR-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1241_BJHR-N1-BDNA-1_A23TNVNLT4_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: 84775785 total, 57360 skipped (flags/unmapped)
Fragments: 42550410 total (42126424 tlen-paired, 3304 hash-paired, 399 singletons, 14939 discordant, 405344 orphans, 11674 too large [>5000 bp], 16910834 duplicates)
Reads: 91941082 total, 48348 skipped (flags/unmapped)
Fragments: 46156067 total (45703885 tlen-paired, 2198 hash-paired, 520 singletons, 11740 discordant, 437724 orphans, 9422 too large [>5000 bp], 17944845 duplicates)
Reads: 91098349 total, 50432 skipped (flags/unmapped)
Fragments: 45732246 total (45265221 tlen-paired, 4575 hash-paired, 367 singletons, 13179 discordant, 448904 orphans, 16348 too large [>5000 bp], 18270176 duplicates)
Reads: 101410803 total, 97003 skipped (flags/unmapped)
Fragments: 51080627 total (49746572 tlen-paired, 3229 hash-paired, 454 singletons, 268464 discordant, 1061908 orphans, 107454 too large [>5000 bp], 20326697 duplicates)