Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_25V-N1-BDNA-1_A23MHW3LT4_1/1136_25V-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/9af57b8a345a31bc800898fe2227c5/.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/d2/9af57b8a345a31bc800898fe2227c5/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_25V-N1-BDNA-1_A23MHW3LT4_1/1136_25V-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
==> 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_25V-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_25V-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_25V-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_25V-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: 103684732 total, 71456 skipped (flags/unmapped)
Fragments: 52055910 total (51504814 tlen-paired, 5037 hash-paired, 593 singletons, 19791 discordant, 525675 orphans, 13862 too large [>5000 bp], 17707011 duplicates)
Reads: 112867521 total, 58537 skipped (flags/unmapped)
Fragments: 56663333 total (56102245 tlen-paired, 3818 hash-paired, 574 singletons, 14110 discordant, 542586 orphans, 12739 too large [>5000 bp], 19009115 duplicates)
Reads: 110218756 total, 64452 skipped (flags/unmapped)
Fragments: 55345211 total (54742940 tlen-paired, 7093 hash-paired, 501 singletons, 16992 discordant, 577685 orphans, 21034 too large [>5000 bp], 19037015 duplicates)
Reads: 122402459 total, 102471 skipped (flags/unmapped)
Fragments: 61679771 total (60010505 tlen-paired, 5934 hash-paired, 625 singletons, 329754 discordant, 1332953 orphans, 137012 too large [>5000 bp], 21179398 duplicates)