Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1136_5YE-N1-BDNA-1_B23L5TMLT4_1/1136_5YE-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/c030a89644c9618de58a3e18e31f1d/.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/8f/c030a89644c9618de58a3e18e31f1d/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1136_5YE-N1-BDNA-1_B23L5TMLT4_1/1136_5YE-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_5YE-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1136_5YE-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5YE-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5YE-N1-BDNA-1_B23L5TMLT4_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: 96576547 total, 71521 skipped (flags/unmapped)
Fragments: 48455025 total (48002359 tlen-paired, 4750 hash-paired, 469 singletons, 16414 discordant, 431033 orphans, 13239 too large [>5000 bp], 18289931 duplicates)
Reads: 101734212 total, 63029 skipped (flags/unmapped)
Fragments: 51051020 total (50544728 tlen-paired, 5929 hash-paired, 480 singletons, 14772 discordant, 485111 orphans, 27367 too large [>5000 bp], 19310564 duplicates)
Reads: 102921686 total, 61532 skipped (flags/unmapped)
Fragments: 51642535 total (51176953 tlen-paired, 3158 hash-paired, 537 singletons, 12296 discordant, 449591 orphans, 12606 too large [>5000 bp], 19159821 duplicates)
Reads: 113032430 total, 113609 skipped (flags/unmapped)
Fragments: 56892932 total (55532856 tlen-paired, 3877 hash-paired, 531 singletons, 268406 discordant, 1087262 orphans, 110375 too large [>5000 bp], 21456996 duplicates)