Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/34/0de3afc23e2024bc318ccdbf26a96f/.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/34/0de3afc23e2024bc318ccdbf26a96f/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_3HZ-N1-BDNA-1_A23NMNVLT4_1/1136_3HZ-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_3HZ-N1-BDNA-1_A23NMNVLT4_1/1136_3HZ-N1-BDNA-1_A23NMNVLT4_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: 1136_3HZ-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3HZ-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3HZ-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_3HZ-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: 96581264 total, 73726 skipped (flags/unmapped)
Fragments: 48370802 total (48094708 tlen-paired, 3554 hash-paired, 407 singletons, 15288 discordant, 256845 orphans, 11593 too large [>5000 bp], 15601046 duplicates)
Reads: 103247973 total, 63187 skipped (flags/unmapped)
Fragments: 51711446 total (51438975 tlen-paired, 2627 hash-paired, 463 singletons, 10278 discordant, 259103 orphans, 10730 too large [>5000 bp], 16480543 duplicates)
Reads: 103807434 total, 65930 skipped (flags/unmapped)
Fragments: 51998943 total (51679641 tlen-paired, 3764 hash-paired, 307 singletons, 13228 discordant, 302003 orphans, 22964 too large [>5000 bp], 17085025 duplicates)
Reads: 114004878 total, 117358 skipped (flags/unmapped)
Fragments: 57169508 total (56455652 tlen-paired, 3557 hash-paired, 466 singletons, 137103 discordant, 572730 orphans, 60850 too large [>5000 bp], 18848937 duplicates)