Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BHR9-N1-BDNA-1_A23TNVNLT4_1/1241_BHR9-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BHR9-N1-BDNA-1_A23TNVNLT4_1/1241_BHR9-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/fa2cde307c99b870899b380d15561e/.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/5a/fa2cde307c99b870899b380d15561e/.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_BHR9-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BHR9-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BHR9-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BHR9-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: 120039064 total, 78081 skipped (flags/unmapped)
Fragments: 60154193 total (59757314 tlen-paired, 6626 hash-paired, 538 singletons, 20434 discordant, 369281 orphans, 11208 too large [>5000 bp], 21871800 duplicates)
Reads: 129850640 total, 66711 skipped (flags/unmapped)
Fragments: 65068783 total (64670321 tlen-paired, 4956 hash-paired, 656 singletons, 14037 discordant, 378813 orphans, 12916 too large [>5000 bp], 23372068 duplicates)
Reads: 140441101 total, 71370 skipped (flags/unmapped)
Fragments: 70375955 total (69912620 tlen-paired, 7404 hash-paired, 518 singletons, 21184 discordant, 434229 orphans, 26284 too large [>5000 bp], 25932006 duplicates)
Reads: 142334248 total, 129812 skipped (flags/unmapped)
Fragments: 71454122 total (70371775 tlen-paired, 5903 hash-paired, 561 singletons, 205552 discordant, 870331 orphans, 83542 too large [>5000 bp], 26337599 duplicates)