Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/17196b9cc4a5cfb8f5c10e23b8caef/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0021/20260113_LH00527_0046_A23FG3YLT4__aa3fd045--20260225-014632/alignments/recalibrated/659_sv-N1-BDNA-1_A23FG3YLT4_1/659_sv-N1-BDNA-1_A23FG3YLT4_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/01/17196b9cc4a5cfb8f5c10e23b8caef/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0021/20260113_LH00527_0046_A23FG3YLT4__aa3fd045--20260225-014632/alignments/recalibrated/659_sv-N1-BDNA-1_A23FG3YLT4_1/659_sv-N1-BDNA-1_A23FG3YLT4_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] [W::hts_idx_load3] The index file is older than the data file: 659_sv-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.baiThe index file is older than the data file: 659_sv-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.baiThe index file is older than the data file: 659_sv-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
The index file is older than the data file: 659_sv-N1-BDNA-1_A23FG3YLT4_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: 51756738 total, 34163 skipped (flags/unmapped)
Fragments: 25951070 total (25755152 tlen-paired, 2108 hash-paired, 275 singletons, 7647 discordant, 185888 orphans, 3299 too large [>5000 bp], 5714040 duplicates)
Reads: 57279908 total, 36374 skipped (flags/unmapped)
Fragments: 28715791 total (28492265 tlen-paired, 2614 hash-paired, 277 singletons, 7520 discordant, 213115 orphans, 12672 too large [>5000 bp], 6242253 duplicates)
Reads: 57949742 total, 53481 skipped (flags/unmapped)
Fragments: 29141500 total (28550782 tlen-paired, 2144 hash-paired, 261 singletons, 112085 discordant, 476228 orphans, 44875 too large [>5000 bp], 6343390 duplicates)
Reads: 56914367 total, 32872 skipped (flags/unmapped)
Fragments: 28535374 total (28323959 tlen-paired, 3251 hash-paired, 381 singletons, 5345 discordant, 202438 orphans, 6783 too large [>5000 bp], 6151890 duplicates)