Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/d9c4802c1d09880de12611f31edeb5/.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/3d/d9c4802c1d09880de12611f31edeb5/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1267_DZ-N1-BDNA-1_A23TNVNLT4_1/1267_DZ-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1267_DZ-N1-BDNA-1_A23TNVNLT4_1/1267_DZ-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1267_DZ-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1267_DZ-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1267_DZ-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1267_DZ-N1-BDNA-1_A23TNVNLT4_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: 77763606 total, 53513 skipped (flags/unmapped)
Fragments: 38966138 total (38708955 tlen-paired, 4109 hash-paired, 317 singletons, 14055 discordant, 238702 orphans, 8418 too large [>5000 bp], 13511906 duplicates)
Reads: 83784025 total, 48149 skipped (flags/unmapped)
Fragments: 41979886 total (41723411 tlen-paired, 4185 hash-paired, 446 singletons, 10006 discordant, 241838 orphans, 9194 too large [>5000 bp], 14310240 duplicates)
Reads: 91673249 total, 85594 skipped (flags/unmapped)
Fragments: 46013461 total (45342471 tlen-paired, 4296 hash-paired, 361 singletons, 124343 discordant, 541990 orphans, 51542 too large [>5000 bp], 16096314 duplicates)
Reads: 91309984 total, 49048 skipped (flags/unmapped)
Fragments: 45753439 total (45461216 tlen-paired, 4727 hash-paired, 311 singletons, 14358 discordant, 272827 orphans, 13598 too large [>5000 bp], 15977866 duplicates)