Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/241711cccdabde93368fb1aeb0787a/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_P1W-N1-BDNA-1_A23TY7KLT4_1/1241_P1W-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam
  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/6e/241711cccdabde93368fb1aeb0787a/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_P1W-N1-BDNA-1_A23TY7KLT4_1/1241_P1W-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
==> 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: 1241_P1W-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_P1W-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_P1W-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_P1W-N1-BDNA-1_A23TY7KLT4_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: 66183532 total, 46282 skipped (flags/unmapped)
Fragments: 33160286 total (32945018 tlen-paired, 2926 hash-paired, 229 singletons, 11306 discordant, 200807 orphans, 8857 too large [>5000 bp], 10868112 duplicates)
Reads: 71431221 total, 38089 skipped (flags/unmapped)
Fragments: 35792719 total (35575694 tlen-paired, 2719 hash-paired, 314 singletons, 8412 discordant, 205580 orphans, 6794 too large [>5000 bp], 11541773 duplicates)
Reads: 70803114 total, 40697 skipped (flags/unmapped)
Fragments: 35479098 total (35236905 tlen-paired, 3467 hash-paired, 210 singletons, 10161 discordant, 228355 orphans, 16393 too large [>5000 bp], 11751800 duplicates)
Reads: 77742662 total, 70080 skipped (flags/unmapped)
Fragments: 39017109 total (38452587 tlen-paired, 2935 hash-paired, 290 singletons, 109365 discordant, 451932 orphans, 45293 too large [>5000 bp], 12933490 duplicates)