Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_268-N1-BDNA-1_A23NLN3LT4_1/1136_268-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a9/d42c2428d7a2bb0c3de9b6ef3541c2/.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/a9/d42c2428d7a2bb0c3de9b6ef3541c2/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_268-N1-BDNA-1_A23NLN3LT4_1/1136_268-N1-BDNA-1_A23NLN3LT4_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_268-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_268-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_268-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_268-N1-BDNA-1_A23NLN3LT4_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: 93417778 total, 67934 skipped (flags/unmapped)
Fragments: 46809799 total (46490350 tlen-paired, 3251 hash-paired, 377 singletons, 19882 discordant, 295939 orphans, 13281 too large [>5000 bp], 16976259 duplicates)
Reads: 99947593 total, 60285 skipped (flags/unmapped)
Fragments: 50092929 total (49721106 tlen-paired, 4863 hash-paired, 311 singletons, 17080 discordant, 349569 orphans, 25665 too large [>5000 bp], 18369221 duplicates)
Reads: 100557192 total, 58121 skipped (flags/unmapped)
Fragments: 50385993 total (50069707 tlen-paired, 4123 hash-paired, 505 singletons, 13426 discordant, 298232 orphans, 12911 too large [>5000 bp], 18023373 duplicates)
Reads: 110211815 total, 105503 skipped (flags/unmapped)
Fragments: 55304338 total (54518951 tlen-paired, 4417 hash-paired, 421 singletons, 149518 discordant, 631031 orphans, 64544 too large [>5000 bp], 20327265 duplicates)