Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00166_0269_A23H3W5LT3__d7a6b981--20260320-054016/alignments/recalibrated/1136_0NH-N1-BDNA-1_A23H3W5LT3_1/1136_0NH-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/29/2a00cb73f3ea924ac26a6befd19e1e/.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/29/2a00cb73f3ea924ac26a6befd19e1e/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00166_0269_A23H3W5LT3__d7a6b981--20260320-054016/alignments/recalibrated/1136_0NH-N1-BDNA-1_A23H3W5LT3_1/1136_0NH-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam
==> 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: 1136_0NH-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0NH-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0NH-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0NH-N1-BDNA-1_A23H3W5LT3_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: 48629379 total, 42365 skipped (flags/unmapped)
Fragments: 24594246 total (23960661 tlen-paired, 2620 hash-paired, 3093 singletons, 4553 discordant, 623319 orphans, 12467 too large [>5000 bp], 4723819 duplicates)
Reads: 48063177 total, 48647 skipped (flags/unmapped)
Fragments: 24296159 total (23700014 tlen-paired, 3349 hash-paired, 3188 singletons, 4918 discordant, 584690 orphans, 5045 too large [>5000 bp], 4689036 duplicates)
Reads: 53404203 total, 44175 skipped (flags/unmapped)
Fragments: 27017210 total (26321885 tlen-paired, 3390 hash-paired, 3501 singletons, 3717 discordant, 684717 orphans, 6913 too large [>5000 bp], 5172850 duplicates)
Reads: 55877664 total, 71912 skipped (flags/unmapped)
Fragments: 28631512 total (26353185 tlen-paired, 3287 hash-paired, 3623 singletons, 461968 discordant, 1809449 orphans, 177900 too large [>5000 bp], 5328279 duplicates)