Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/f4374b0029be97b5103588615b6d58/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0021/20260113_LH00527_0046_A23FG3YLT4__aa3fd045--20260225-014632/alignments/recalibrated/869_EH0-N1-BDNA-1_A23FG3YLT4_1/869_EH0-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/ba/f4374b0029be97b5103588615b6d58/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0021/20260113_LH00527_0046_A23FG3YLT4__aa3fd045--20260225-014632/alignments/recalibrated/869_EH0-N1-BDNA-1_A23FG3YLT4_1/869_EH0-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] The index file is older than the data file: 869_EH0-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_EH0-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_EH0-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_EH0-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: 74067152 total, 52531 skipped (flags/unmapped)
Fragments: 37127430 total (36860211 tlen-paired, 3410 hash-paired, 357 singletons, 11798 discordant, 251654 orphans, 5886 too large [>5000 bp], 9322222 duplicates)
Reads: 82661977 total, 74426 skipped (flags/unmapped)
Fragments: 41542749 total (40789418 tlen-paired, 2604 hash-paired, 374 singletons, 141596 discordant, 608757 orphans, 55592 too large [>5000 bp], 10329494 duplicates)
Reads: 81625804 total, 53511 skipped (flags/unmapped)
Fragments: 40911836 total (40602684 tlen-paired, 5833 hash-paired, 426 singletons, 12030 discordant, 290863 orphans, 19955 too large [>5000 bp], 10162323 duplicates)
Reads: 80782961 total, 49925 skipped (flags/unmapped)
Fragments: 40491992 total (40208759 tlen-paired, 4171 hash-paired, 392 singletons, 8550 discordant, 270120 orphans, 9782 too large [>5000 bp], 9998384 duplicates)