Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/2bf0b935887dfc4bd932b88917fe37/.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/8e/2bf0b935887dfc4bd932b88917fe37/.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_5Q0-N1-BDNA-1_A23TY32LT4_1/1241_5Q0-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_5Q0-N1-BDNA-1_A23TY32LT4_1/1241_5Q0-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] [W::hts_idx_load3] The index file is older than the data file: 1241_5Q0-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1241_5Q0-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1241_5Q0-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_5Q0-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: 87434796 total, 62262 skipped (flags/unmapped)
Fragments: 43871499 total (43459667 tlen-paired, 3833 hash-paired, 415 singletons, 11243 discordant, 396341 orphans, 13146 too large [>5000 bp], 18976339 duplicates)
Reads: 94009394 total, 53351 skipped (flags/unmapped)
Fragments: 47181765 total (46741419 tlen-paired, 3466 hash-paired, 449 singletons, 7879 discordant, 428552 orphans, 10757 too large [>5000 bp], 20050812 duplicates)
Reads: 103262050 total, 57028 skipped (flags/unmapped)
Fragments: 51823028 total (51344502 tlen-paired, 3942 hash-paired, 325 singletons, 11522 discordant, 462737 orphans, 11014 too large [>5000 bp], 22524901 duplicates)
Reads: 105202356 total, 104080 skipped (flags/unmapped)
Fragments: 52994833 total (51596738 tlen-paired, 3929 hash-paired, 366 singletons, 280070 discordant, 1113730 orphans, 111353 too large [>5000 bp], 22863855 duplicates)