Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0021/20260113_LH00527_0046_A23FG3YLT4__aa3fd045--20260225-014632/alignments/recalibrated/659_eZ3-N1-BDNA-1_A23FG3YLT4_1/659_eZ3-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/9b8514ddc861ac7aa3b433ae0bf84c/.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/b2/9b8514ddc861ac7aa3b433ae0bf84c/.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_eZ3-N1-BDNA-1_A23FG3YLT4_1/659_eZ3-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 659_eZ3-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 659_eZ3-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eZ3-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eZ3-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: 55495353 total, 41810 skipped (flags/unmapped)
Fragments: 27812787 total (27621985 tlen-paired, 2664 hash-paired, 283 singletons, 8423 discordant, 179432 orphans, 3842 too large [>5000 bp], 6216055 duplicates)
Reads: 61800343 total, 64210 skipped (flags/unmapped)
Fragments: 31045408 total (30502017 tlen-paired, 2299 hash-paired, 311 singletons, 101559 discordant, 439222 orphans, 42425 too large [>5000 bp], 6885136 duplicates)
Reads: 61273708 total, 39413 skipped (flags/unmapped)
Fragments: 30707293 total (30497463 tlen-paired, 2851 hash-paired, 261 singletons, 8202 discordant, 198516 orphans, 9243 too large [>5000 bp], 6795327 duplicates)
Reads: 61207366 total, 36553 skipped (flags/unmapped)
Fragments: 30675056 total (30473175 tlen-paired, 1891 hash-paired, 323 singletons, 6089 discordant, 193578 orphans, 7301 too large [>5000 bp], 6754730 duplicates)