Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_0GF-N1-BDNA-1_A23MHW3LT4_1/1136_0GF-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/957b3539b9167487ff26c70d07bf7f/.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/d3/957b3539b9167487ff26c70d07bf7f/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_0GF-N1-BDNA-1_A23MHW3LT4_1/1136_0GF-N1-BDNA-1_A23MHW3LT4_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_0GF-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0GF-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0GF-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0GF-N1-BDNA-1_A23MHW3LT4_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: 88402845 total, 67677 skipped (flags/unmapped)
Fragments: 44415700 total (43878040 tlen-paired, 4018 hash-paired, 551 singletons, 13532 discordant, 519559 orphans, 11939 too large [>5000 bp], 16351081 duplicates)
Reads: 92346150 total, 63975 skipped (flags/unmapped)
Fragments: 46408843 total (45809535 tlen-paired, 5199 hash-paired, 529 singletons, 11780 discordant, 581800 orphans, 23409 too large [>5000 bp], 17088741 duplicates)
Reads: 93652680 total, 61584 skipped (flags/unmapped)
Fragments: 47057146 total (46494440 tlen-paired, 3817 hash-paired, 625 singletons, 10327 discordant, 547937 orphans, 12683 too large [>5000 bp], 16882771 duplicates)
Reads: 102871187 total, 106727 skipped (flags/unmapped)
Fragments: 51938478 total (50170616 tlen-paired, 2951 hash-paired, 519 singletons, 354281 discordant, 1410111 orphans, 149067 too large [>5000 bp], 19003471 duplicates)