Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/4358837a9e2cb736f749efa9f48e59/.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/52/4358837a9e2cb736f749efa9f48e59/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_FSL-N1-BDNA-1_A23TY7KLT4_1/1241_FSL-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_FSL-N1-BDNA-1_A23TY7KLT4_1/1241_FSL-N1-BDNA-1_A23TY7KLT4_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: 1241_FSL-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_FSL-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_FSL-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_FSL-N1-BDNA-1_A23TY7KLT4_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: 101800726 total, 57289 skipped (flags/unmapped)
Fragments: 50982201 total (50723255 tlen-paired, 4514 hash-paired, 467 singletons, 10511 discordant, 243454 orphans, 11478 too large [>5000 bp], 18017726 duplicates)
Reads: 96080350 total, 69881 skipped (flags/unmapped)
Fragments: 48113476 total (47852606 tlen-paired, 5291 hash-paired, 430 singletons, 14800 discordant, 240349 orphans, 12148 too large [>5000 bp], 17306659 duplicates)
Reads: 101746310 total, 58923 skipped (flags/unmapped)
Fragments: 50962506 total (50673319 tlen-paired, 3589 hash-paired, 306 singletons, 12659 discordant, 272633 orphans, 17657 too large [>5000 bp], 18434507 duplicates)
Reads: 111796100 total, 109698 skipped (flags/unmapped)
Fragments: 56044220 total (55395045 tlen-paired, 7061 hash-paired, 420 singletons, 121994 discordant, 519700 orphans, 59041 too large [>5000 bp], 20300687 duplicates)