Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/9ee38266cf5ee268d2e6e0d2c3cec9/.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/f8/9ee38266cf5ee268d2e6e0d2c3cec9/.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_MJX-N1-BDNA-1_A23FG3YLT4_1/869_MJX-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0021/20260113_LH00527_0046_A23FG3YLT4__aa3fd045--20260225-014632/alignments/recalibrated/869_MJX-N1-BDNA-1_A23FG3YLT4_1/869_MJX-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: 869_MJX-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_MJX-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 869_MJX-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_MJX-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: 62885499 total, 41193 skipped (flags/unmapped)
Fragments: 31523561 total (31299563 tlen-paired, 2368 hash-paired, 348 singletons, 9588 discordant, 211694 orphans, 4613 too large [>5000 bp], 7339514 duplicates)
Reads: 63171375 total, 39247 skipped (flags/unmapped)
Fragments: 31664956 total (31425857 tlen-paired, 2497 hash-paired, 310 singletons, 7702 discordant, 228590 orphans, 15558 too large [>5000 bp], 7304552 duplicates)
Reads: 69478368 total, 38526 skipped (flags/unmapped)
Fragments: 34828088 total (34585865 tlen-paired, 3273 hash-paired, 426 singletons, 6910 discordant, 231614 orphans, 7853 too large [>5000 bp], 7976689 duplicates)
Reads: 70224605 total, 64507 skipped (flags/unmapped)
Fragments: 35290783 total (34642511 tlen-paired, 2715 hash-paired, 366 singletons, 124783 discordant, 520408 orphans, 49653 too large [>5000 bp], 8146893 duplicates)