Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/dfd8ea8ef88375758abf612599c4d9/.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/ee/dfd8ea8ef88375758abf612599c4d9/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_6GL-N1-BDNA-1_A23NMNVLT4_1/1136_6GL-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_6GL-N1-BDNA-1_A23NMNVLT4_1/1136_6GL-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_6GL-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6GL-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_6GL-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6GL-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: 71235165 total, 54026 skipped (flags/unmapped)
Fragments: 35675407 total (35478333 tlen-paired, 3652 hash-paired, 360 singletons, 9503 discordant, 183559 orphans, 7122 too large [>5000 bp], 10686120 duplicates)
Reads: 77179958 total, 47832 skipped (flags/unmapped)
Fragments: 38658127 total (38440602 tlen-paired, 4369 hash-paired, 292 singletons, 8128 discordant, 204736 orphans, 10450 too large [>5000 bp], 11723559 duplicates)
Reads: 77015107 total, 46864 skipped (flags/unmapped)
Fragments: 38571154 total (38372233 tlen-paired, 2787 hash-paired, 302 singletons, 6663 discordant, 189169 orphans, 7703 too large [>5000 bp], 11336057 duplicates)
Reads: 84537188 total, 79877 skipped (flags/unmapped)
Fragments: 42400868 total (41862144 tlen-paired, 2567 hash-paired, 354 singletons, 104416 discordant, 431387 orphans, 43658 too large [>5000 bp], 12876985 duplicates)