Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/1edb2e3f65ef450b4b20fd44a89bbf/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_BDKA-N1-BDNA-1_A23TY32LT4_1/1241_BDKA-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/a0/1edb2e3f65ef450b4b20fd44a89bbf/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_BDKA-N1-BDNA-1_A23TY32LT4_1/1241_BDKA-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1241_BDKA-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BDKA-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BDKA-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1241_BDKA-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: 81202338 total, 58202 skipped (flags/unmapped)
Fragments: 40721171 total (40389295 tlen-paired, 3144 hash-paired, 351 singletons, 13312 discordant, 315069 orphans, 8607 too large [>5000 bp], 15615189 duplicates)
Reads: 87888998 total, 50547 skipped (flags/unmapped)
Fragments: 44080113 total (43698944 tlen-paired, 2621 hash-paired, 263 singletons, 11823 discordant, 366462 orphans, 22475 too large [>5000 bp], 16961272 duplicates)
Reads: 88231878 total, 53283 skipped (flags/unmapped)
Fragments: 44248354 total (43897765 tlen-paired, 3205 hash-paired, 465 singletons, 9311 discordant, 337608 orphans, 9980 too large [>5000 bp], 16634453 duplicates)
Reads: 97301580 total, 101337 skipped (flags/unmapped)
Fragments: 48918399 total (47910833 tlen-paired, 4080 hash-paired, 348 singletons, 200835 discordant, 802303 orphans, 83048 too large [>5000 bp], 18793387 duplicates)