Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1173_NMN-N1-BDNA-01_A23MHW3LT4_1/1173_NMN-N1-BDNA-01_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/d3ff5eaa672e9081d5d58fb57493df/.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/51/d3ff5eaa672e9081d5d58fb57493df/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1173_NMN-N1-BDNA-01_A23MHW3LT4_1/1173_NMN-N1-BDNA-01_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] The index file is older than the data file: 1173_NMN-N1-BDNA-01_A23MHW3LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1173_NMN-N1-BDNA-01_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_NMN-N1-BDNA-01_A23MHW3LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1173_NMN-N1-BDNA-01_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: 39800336 total, 50953 skipped (flags/unmapped)
Fragments: 20310920 total (19416371 tlen-paired, 3441 hash-paired, 289 singletons, 4839 discordant, 885980 orphans, 6906 too large [>5000 bp], 9097295 duplicates)
Reads: 40833597 total, 50321 skipped (flags/unmapped)
Fragments: 20841802 total (19921833 tlen-paired, 2956 hash-paired, 317 singletons, 3535 discordant, 913161 orphans, 6575 too large [>5000 bp], 9112245 duplicates)
Reads: 45425162 total, 51854 skipped (flags/unmapped)
Fragments: 23183081 total (22153268 tlen-paired, 3572 hash-paired, 280 singletons, 5069 discordant, 1020892 orphans, 14159 too large [>5000 bp], 10376580 duplicates)
Reads: 49144138 total, 86979 skipped (flags/unmapped)
Fragments: 25606118 total (22172728 tlen-paired, 2490 hash-paired, 419 singletons, 690599 discordant, 2739882 orphans, 292612 too large [>5000 bp], 10823471 duplicates)