Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_7Q0-N1-BDNA-1_A23NLN3LT4_1/1136_7Q0-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_7Q0-N1-BDNA-1_A23NLN3LT4_1/1136_7Q0-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/f5cf136f4730c37aa687302a70cd60/.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/c4/f5cf136f4730c37aa687302a70cd60/.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_7Q0-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7Q0-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7Q0-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7Q0-N1-BDNA-1_A23NLN3LT4_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: 77385146 total, 58330 skipped (flags/unmapped)
Fragments: 38821610 total (38468487 tlen-paired, 3695 hash-paired, 393 singletons, 11044 discordant, 337991 orphans, 10990 too large [>5000 bp], 14551001 duplicates)
Reads: 82675296 total, 50144 skipped (flags/unmapped)
Fragments: 41481821 total (41109241 tlen-paired, 2908 hash-paired, 492 singletons, 8798 discordant, 360382 orphans, 11192 too large [>5000 bp], 15180768 duplicates)
Reads: 83258810 total, 51924 skipped (flags/unmapped)
Fragments: 41782447 total (41357363 tlen-paired, 5263 hash-paired, 304 singletons, 10979 discordant, 408538 orphans, 25417 too large [>5000 bp], 15715692 duplicates)
Reads: 91702623 total, 88647 skipped (flags/unmapped)
Fragments: 46158666 total (45036959 tlen-paired, 3157 hash-paired, 347 singletons, 224322 discordant, 893881 orphans, 95436 too large [>5000 bp], 17325624 duplicates)