Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/bf6719824c68794d650d039871d771/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/659_cJ6-N1-BDNA-1_A23TY32LT4_1/659_cJ6-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
  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/db/bf6719824c68794d650d039871d771/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/659_cJ6-N1-BDNA-1_A23TY32LT4_1/659_cJ6-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
==> 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: 659_cJ6-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cJ6-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cJ6-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cJ6-N1-BDNA-1_A23TY32LT4_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: 100166905 total, 80037 skipped (flags/unmapped)
Fragments: 50259444 total (49773838 tlen-paired, 5121 hash-paired, 443 singletons, 19399 discordant, 460643 orphans, 14533 too large [>5000 bp], 20434182 duplicates)
Reads: 107596621 total, 72331 skipped (flags/unmapped)
Fragments: 53991112 total (53485106 tlen-paired, 5511 hash-paired, 420 singletons, 13777 discordant, 486298 orphans, 14392 too large [>5000 bp], 21624993 duplicates)
Reads: 118214180 total, 74361 skipped (flags/unmapped)
Fragments: 59324591 total (58741147 tlen-paired, 6663 hash-paired, 410 singletons, 19780 discordant, 556591 orphans, 23819 too large [>5000 bp], 24318826 duplicates)
Reads: 120245711 total, 127220 skipped (flags/unmapped)
Fragments: 60535685 total (59052297 tlen-paired, 5195 hash-paired, 426 singletons, 290186 discordant, 1187581 orphans, 117564 too large [>5000 bp], 24710323 duplicates)