Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/fee20b0d85afb24e859362817e4be1/.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/c9/fee20b0d85afb24e859362817e4be1/.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_BL7I-N1-BDNA-1_A23TY32LT4_1/1241_BL7I-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_BL7I-N1-BDNA-1_A23TY32LT4_1/1241_BL7I-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
==> 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_BL7I-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1241_BL7I-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1241_BL7I-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BL7I-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: 45237686 total, 34782 skipped (flags/unmapped)
Fragments: 22719238 total (22463520 tlen-paired, 1987 hash-paired, 174 singletons, 6051 discordant, 247506 orphans, 6054 too large [>5000 bp], 9239587 duplicates)
Reads: 48387731 total, 29155 skipped (flags/unmapped)
Fragments: 24309740 total (24032127 tlen-paired, 1489 hash-paired, 245 singletons, 4472 discordant, 271407 orphans, 5374 too large [>5000 bp], 9699278 duplicates)
Reads: 53529570 total, 31290 skipped (flags/unmapped)
Fragments: 26891014 total (26574206 tlen-paired, 2885 hash-paired, 155 singletons, 6291 discordant, 307477 orphans, 11942 too large [>5000 bp], 10924235 duplicates)
Reads: 54478047 total, 61386 skipped (flags/unmapped)
Fragments: 27496922 total (26590730 tlen-paired, 2462 hash-paired, 205 singletons, 182221 discordant, 721304 orphans, 72163 too large [>5000 bp], 11070231 duplicates)