Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_3CE-N1-BDNA-1_A23NMNVLT4_1/1136_3CE-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_3CE-N1-BDNA-1_A23NMNVLT4_1/1136_3CE-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/270a609062947d71ef55ef3dced30f/.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/a1/270a609062947d71ef55ef3dced30f/.command.run
==> 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_3CE-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3CE-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3CE-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3CE-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: 72176688 total, 57635 skipped (flags/unmapped)
Fragments: 36156961 total (35928706 tlen-paired, 3350 hash-paired, 332 singletons, 11352 discordant, 213221 orphans, 9342 too large [>5000 bp], 10394263 duplicates)
Reads: 76569398 total, 46672 skipped (flags/unmapped)
Fragments: 38360100 total (38134818 tlen-paired, 2843 hash-paired, 317 singletons, 7723 discordant, 214399 orphans, 8621 too large [>5000 bp], 10895088 duplicates)
Reads: 85636622 total, 87829 skipped (flags/unmapped)
Fragments: 42972407 total (42358953 tlen-paired, 2919 hash-paired, 351 singletons, 115628 discordant, 494556 orphans, 49443 too large [>5000 bp], 12509646 duplicates)
Reads: 84827092 total, 52833 skipped (flags/unmapped)
Fragments: 42500625 total (42211954 tlen-paired, 3607 hash-paired, 290 singletons, 11949 discordant, 272825 orphans, 23062 too large [>5000 bp], 12370012 duplicates)