Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/42/2c9729487d364c1e525011fbc07356/.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/42/2c9729487d364c1e525011fbc07356/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_7G1-N1-BDNA-1_A23NMNVLT4_1/1136_7G1-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_7G1-N1-BDNA-1_A23NMNVLT4_1/1136_7G1-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
==> 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: 1136_7G1-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7G1-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7G1-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7G1-N1-BDNA-1_A23NMNVLT4_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: 81584397 total, 54591 skipped (flags/unmapped)
Fragments: 40873117 total (40620100 tlen-paired, 3716 hash-paired, 398 singletons, 12543 discordant, 236360 orphans, 10165 too large [>5000 bp], 10127070 duplicates)
Reads: 87498548 total, 42310 skipped (flags/unmapped)
Fragments: 43840323 total (43589515 tlen-paired, 2476 hash-paired, 357 singletons, 8746 discordant, 239229 orphans, 7589 too large [>5000 bp], 10706371 duplicates)
Reads: 95815259 total, 47616 skipped (flags/unmapped)
Fragments: 48008742 total (47709545 tlen-paired, 3630 hash-paired, 293 singletons, 12872 discordant, 282402 orphans, 16427 too large [>5000 bp], 12120125 duplicates)
Reads: 96201723 total, 75853 skipped (flags/unmapped)
Fragments: 48286454 total (47597458 tlen-paired, 3024 hash-paired, 449 singletons, 130066 discordant, 555457 orphans, 54434 too large [>5000 bp], 12212348 duplicates)