Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/dc6526e53c74349a54a167dcf5e62b/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260309_LH00166_0264_B23H3Y2LT3__5d7f62c6--20260311-041011/alignments/recalibrated/869_IMN-N1-BDNA-1_B23H3Y2LT3_1/869_IMN-N1-BDNA-1_B23H3Y2LT3_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/fe/dc6526e53c74349a54a167dcf5e62b/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260309_LH00166_0264_B23H3Y2LT3__5d7f62c6--20260311-041011/alignments/recalibrated/869_IMN-N1-BDNA-1_B23H3Y2LT3_1/869_IMN-N1-BDNA-1_B23H3Y2LT3_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: 869_IMN-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_IMN-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_IMN-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_IMN-N1-BDNA-1_B23H3Y2LT3_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: 76390698 total, 81116 skipped (flags/unmapped)
Fragments: 38389627 total (37877903 tlen-paired, 11860 hash-paired, 2597 singletons, 8992 discordant, 488275 orphans, 10600 too large [>5000 bp], 7876523 duplicates)
Reads: 82886180 total, 66427 skipped (flags/unmapped)
Fragments: 41673688 total (41112941 tlen-paired, 10925 hash-paired, 2765 singletons, 6467 discordant, 540590 orphans, 7866 too large [>5000 bp], 8522758 duplicates)
Reads: 83854755 total, 70284 skipped (flags/unmapped)
Fragments: 42156559 total (41577676 tlen-paired, 11672 hash-paired, 2679 singletons, 9014 discordant, 555518 orphans, 14775 too large [>5000 bp], 8590139 duplicates)
Reads: 86821695 total, 176935 skipped (flags/unmapped)
Fragments: 43903947 total (42099543 tlen-paired, 12082 hash-paired, 2964 singletons, 352236 discordant, 1437122 orphans, 138476 too large [>5000 bp], 8816452 duplicates)