Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_0ET-N1-BDNA-1_A23KFG7LT4_1/1136_0ET-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_0ET-N1-BDNA-1_A23KFG7LT4_1/1136_0ET-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/3dc3207adbe89ed82f6fa14f0bba06/.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/3dc3207adbe89ed82f6fa14f0bba06/.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: 1136_0ET-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_0ET-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1136_0ET-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0ET-N1-BDNA-1_A23KFG7LT4_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: 66237304 total, 46218 skipped (flags/unmapped)
Fragments: 33187623 total (32972156 tlen-paired, 3005 hash-paired, 266 singletons, 10394 discordant, 201802 orphans, 8954 too large [>5000 bp], 10914064 duplicates)
Reads: 70696667 total, 36695 skipped (flags/unmapped)
Fragments: 35427766 total (35209196 tlen-paired, 1975 hash-paired, 449 singletons, 6751 discordant, 209395 orphans, 7142 too large [>5000 bp], 11337333 duplicates)
Reads: 77059691 total, 42127 skipped (flags/unmapped)
Fragments: 38618697 total (38351214 tlen-paired, 3146 hash-paired, 292 singletons, 10391 discordant, 253654 orphans, 17058 too large [>5000 bp], 12719074 duplicates)
Reads: 77883123 total, 70776 skipped (flags/unmapped)
Fragments: 39104061 total (38493872 tlen-paired, 2604 hash-paired, 317 singletons, 116340 discordant, 490928 orphans, 47735 too large [>5000 bp], 12890718 duplicates)