Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0021/20260113_LH00527_0046_A23FG3YLT4__aa3fd045--20260225-014632/alignments/recalibrated/659_btT-N1-BDNA-1_A23FG3YLT4_1/659_btT-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/7fcbcad42cc5136adf5b5e8f02a2ce/.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/45/7fcbcad42cc5136adf5b5e8f02a2ce/.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_btT-N1-BDNA-1_A23FG3YLT4_1/659_btT-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 659_btT-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 659_btT-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_btT-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_btT-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: 57143630 total, 41578 skipped (flags/unmapped)
Fragments: 28636367 total (28436304 tlen-paired, 3718 hash-paired, 271 singletons, 7107 discordant, 188967 orphans, 9278 too large [>5000 bp], 6606754 duplicates)
Reads: 56855420 total, 43705 skipped (flags/unmapped)
Fragments: 28492916 total (28298161 tlen-paired, 2872 hash-paired, 294 singletons, 8880 discordant, 182709 orphans, 4443 too large [>5000 bp], 6645787 duplicates)
Reads: 63267056 total, 63341 skipped (flags/unmapped)
Fragments: 31779227 total (31235824 tlen-paired, 2991 hash-paired, 278 singletons, 103469 discordant, 436665 orphans, 41102 too large [>5000 bp], 7338141 duplicates)
Reads: 62608649 total, 39396 skipped (flags/unmapped)
Fragments: 31376996 total (31167834 tlen-paired, 3211 hash-paired, 370 singletons, 6394 discordant, 199187 orphans, 7409 too large [>5000 bp], 7166852 duplicates)