Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1267_FC-N1-BDNA-1_A23TNVNLT4_1/1267_FC-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/7bb1ba9cb7573d6a93c789461f2a0c/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1267_FC-N1-BDNA-1_A23TNVNLT4_1/1267_FC-N1-BDNA-1_A23TNVNLT4_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/0d/7bb1ba9cb7573d6a93c789461f2a0c/.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: 1267_FC-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1267_FC-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1267_FC-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1267_FC-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: 60007936 total, 42587 skipped (flags/unmapped)
Fragments: 30108641 total (29831064 tlen-paired, 2451 hash-paired, 265 singletons, 8881 discordant, 265980 orphans, 7156 too large [>5000 bp], 11320652 duplicates)
Reads: 64980918 total, 38003 skipped (flags/unmapped)
Fragments: 32611319 total (32309187 tlen-paired, 2399 hash-paired, 385 singletons, 6184 discordant, 293164 orphans, 6913 too large [>5000 bp], 11941130 duplicates)
Reads: 70945459 total, 40859 skipped (flags/unmapped)
Fragments: 35603291 total (35260189 tlen-paired, 3610 hash-paired, 289 singletons, 9262 discordant, 329941 orphans, 14124 too large [>5000 bp], 13403450 duplicates)
Reads: 72227973 total, 75070 skipped (flags/unmapped)
Fragments: 36375459 total (35445773 tlen-paired, 2535 hash-paired, 324 singletons, 185054 discordant, 741773 orphans, 72041 too large [>5000 bp], 13641443 duplicates)