Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/30d4c819bb63c1f1015196f46af304/.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_BOVC-N1-BDNA-1_A23TY32LT4_1/1241_BOVC-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_BOVC-N1-BDNA-1_A23TY32LT4_1/1241_BOVC-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/73/30d4c819bb63c1f1015196f46af304/.command.run
==> 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_BOVC-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BOVC-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BOVC-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BOVC-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: 100612442 total, 76927 skipped (flags/unmapped)
Fragments: 50524618 total (49966321 tlen-paired, 3657 hash-paired, 506 singletons, 15097 discordant, 539037 orphans, 12911 too large [>5000 bp], 23170770 duplicates)
Reads: 107371839 total, 69999 skipped (flags/unmapped)
Fragments: 53926463 total (53332298 tlen-paired, 5145 hash-paired, 567 singletons, 10494 discordant, 577959 orphans, 13720 too large [>5000 bp], 24354959 duplicates)
Reads: 119187278 total, 72175 skipped (flags/unmapped)
Fragments: 59858492 total (59176631 tlen-paired, 4449 hash-paired, 396 singletons, 15725 discordant, 661291 orphans, 29903 too large [>5000 bp], 27565963 duplicates)
Reads: 121349854 total, 138221 skipped (flags/unmapped)
Fragments: 61216260 total (59302374 tlen-paired, 4630 hash-paired, 485 singletons, 382209 discordant, 1526562 orphans, 153080 too large [>5000 bp], 27959149 duplicates)