Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/5835f2f688691e4e01b405e661a8a8/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_0D1-N1-BDNA-1_A23MHW3LT4_1/1136_0D1-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_0D1-N1-BDNA-1_A23MHW3LT4_1/1136_0D1-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  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/36/5835f2f688691e4e01b405e661a8a8/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_0D1-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_0D1-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0D1-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_0D1-N1-BDNA-1_A23MHW3LT4_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: 58233589 total, 37885 skipped (flags/unmapped)
Fragments: 29230260 total (28940099 tlen-paired, 2418 hash-paired, 375 singletons, 6399 discordant, 280969 orphans, 8264 too large [>5000 bp], 8817091 duplicates)
Reads: 55090629 total, 43485 skipped (flags/unmapped)
Fragments: 27652363 total (27365130 tlen-paired, 2293 hash-paired, 313 singletons, 9538 discordant, 275089 orphans, 8910 too large [>5000 bp], 8585019 duplicates)
Reads: 63459909 total, 40903 skipped (flags/unmapped)
Fragments: 31857393 total (31511988 tlen-paired, 4107 hash-paired, 295 singletons, 9686 discordant, 331317 orphans, 17916 too large [>5000 bp], 9880290 duplicates)
Reads: 64490995 total, 64807 skipped (flags/unmapped)
Fragments: 32500128 total (31599898 tlen-paired, 2388 hash-paired, 329 singletons, 174616 discordant, 722897 orphans, 74579 too large [>5000 bp], 10069371 duplicates)