Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0021/20260113_LH00527_0046_A23FG3YLT4__aa3fd045--20260225-014632/alignments/recalibrated/659_b6L-N1-BDNA-1_A23FG3YLT4_1/659_b6L-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/411ee9359b00c9ad84e8bdb04e999a/.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/6e/411ee9359b00c9ad84e8bdb04e999a/.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_b6L-N1-BDNA-1_A23FG3YLT4_1/659_b6L-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_b6L-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_b6L-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b6L-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b6L-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: 53393363 total, 37605 skipped (flags/unmapped)
Fragments: 26763130 total (26565979 tlen-paired, 3054 hash-paired, 265 singletons, 6645 discordant, 187187 orphans, 8475 too large [>5000 bp], 5934130 duplicates)
Reads: 52914729 total, 38731 skipped (flags/unmapped)
Fragments: 26526093 total (26330897 tlen-paired, 2499 hash-paired, 309 singletons, 8357 discordant, 184031 orphans, 4076 too large [>5000 bp], 5936603 duplicates)
Reads: 58486494 total, 35410 skipped (flags/unmapped)
Fragments: 29318796 total (29108510 tlen-paired, 2970 hash-paired, 324 singletons, 6032 discordant, 200960 orphans, 7388 too large [>5000 bp], 6446671 duplicates)
Reads: 59144316 total, 57760 skipped (flags/unmapped)
Fragments: 29726285 total (29163004 tlen-paired, 1867 hash-paired, 302 singletons, 108376 discordant, 452736 orphans, 43512 too large [>5000 bp], 6592138 duplicates)