Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/3767b2b2e9a1f4623fab53020a22e8/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_5SV-N1-BDNA-1_B23KFG5LT4_1/1136_5SV-N1-BDNA-1_B23KFG5LT4_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/a0/3767b2b2e9a1f4623fab53020a22e8/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_5SV-N1-BDNA-1_B23KFG5LT4_1/1136_5SV-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
==> 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_5SV-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5SV-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5SV-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5SV-N1-BDNA-1_B23KFG5LT4_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: 74156755 total, 57686 skipped (flags/unmapped)
Fragments: 37181643 total (36876905 tlen-paired, 2883 hash-paired, 305 singletons, 15708 discordant, 285842 orphans, 10965 too large [>5000 bp], 15305044 duplicates)
Reads: 77472468 total, 48299 skipped (flags/unmapped)
Fragments: 38848970 total (38543309 tlen-paired, 2478 hash-paired, 476 singletons, 10966 discordant, 291741 orphans, 9223 too large [>5000 bp], 15632430 duplicates)
Reads: 87170081 total, 86700 skipped (flags/unmapped)
Fragments: 43808688 total (42986628 tlen-paired, 2079 hash-paired, 365 singletons, 155802 discordant, 663814 orphans, 65092 too large [>5000 bp], 18057580 duplicates)
Reads: 86640043 total, 54324 skipped (flags/unmapped)
Fragments: 43442749 total (43074604 tlen-paired, 3433 hash-paired, 340 singletons, 16617 discordant, 347755 orphans, 24158 too large [>5000 bp], 17888447 duplicates)