Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/562fa0e6f4930b8310e6dbadeec205/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00166_0269_A23H3W5LT3__d7a6b981--20260320-054016/alignments/recalibrated/1136_8FN-N1-BDNA-1_A23H3W5LT3_1/1136_8FN-N1-BDNA-1_A23H3W5LT3_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/97/562fa0e6f4930b8310e6dbadeec205/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00166_0269_A23H3W5LT3__d7a6b981--20260320-054016/alignments/recalibrated/1136_8FN-N1-BDNA-1_A23H3W5LT3_1/1136_8FN-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] [W::hts_idx_load3] The index file is older than the data file: 1136_8FN-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
The index file is older than the data file: 1136_8FN-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_8FN-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_8FN-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: 81772033 total, 60509 skipped (flags/unmapped)
Fragments: 41025319 total (40636199 tlen-paired, 13775 hash-paired, 5527 singletons, 7419 discordant, 362399 orphans, 14406 too large [>5000 bp], 8471145 duplicates)
Reads: 81476531 total, 69566 skipped (flags/unmapped)
Fragments: 40866867 total (40500097 tlen-paired, 14034 hash-paired, 5733 singletons, 8673 discordant, 338330 orphans, 8647 too large [>5000 bp], 8484117 duplicates)
Reads: 89330881 total, 62313 skipped (flags/unmapped)
Fragments: 44818632 total (44411462 tlen-paired, 14979 hash-paired, 6117 singletons, 6351 discordant, 379723 orphans, 8572 too large [>5000 bp], 9262712 duplicates)
Reads: 91329844 total, 107479 skipped (flags/unmapped)
Fragments: 45991130 total (44796228 tlen-paired, 15399 hash-paired, 6372 singletons, 233574 discordant, 939557 orphans, 93017 too large [>5000 bp], 9451531 duplicates)