Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_067-N1-BDNA-1_A23MHW3LT4_1/1136_067-N1-BDNA-1_A23MHW3LT4_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/3d/0d2d7ce180705a39f517d6499ef102/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/0d2d7ce180705a39f517d6499ef102/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_067-N1-BDNA-1_A23MHW3LT4_1/1136_067-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] [W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_067-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_067-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_067-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai


[W::hts_idx_load3] The index file is older than the data file: 1136_067-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: 82841390 total, 64465 skipped (flags/unmapped)
Fragments: 41676416 total (41056882 tlen-paired, 3649 hash-paired, 549 singletons, 15436 discordant, 599900 orphans, 12271 too large [>5000 bp], 16129569 duplicates)
Reads: 88029611 total, 59648 skipped (flags/unmapped)
Fragments: 44285933 total (43640307 tlen-paired, 3512 hash-paired, 653 singletons, 11351 discordant, 630110 orphans, 14430 too large [>5000 bp], 16670584 duplicates)
Reads: 87199036 total, 57895 skipped (flags/unmapped)
Fragments: 43876683 total (43206437 tlen-paired, 3180 hash-paired, 457 singletons, 13521 discordant, 653088 orphans, 20660 too large [>5000 bp], 16977018 duplicates)
Reads: 97547340 total, 95209 skipped (flags/unmapped)
Fragments: 49373452 total (47317549 tlen-paired, 4106 hash-paired, 480 singletons, 414646 discordant, 1636671 orphans, 171189 too large [>5000 bp], 18989137 duplicates)