Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_00D-N1-BDNA-1_A23MHW3LT4_1/1136_00D-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2f/8e146d38626ba48a48aa9b29e7461a/.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/2f/8e146d38626ba48a48aa9b29e7461a/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_00D-N1-BDNA-1_A23MHW3LT4_1/1136_00D-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
==> 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_00D-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_00D-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_00D-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_00D-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: 71420376 total, 59093 skipped (flags/unmapped)
Fragments: 35917605 total (35407532 tlen-paired, 3157 hash-paired, 358 singletons, 13559 discordant, 492999 orphans, 9715 too large [>5000 bp], 12419437 duplicates)
Reads: 75608737 total, 51604 skipped (flags/unmapped)
Fragments: 38023600 total (37500844 tlen-paired, 2866 hash-paired, 448 singletons, 9511 discordant, 509931 orphans, 10156 too large [>5000 bp], 12851009 duplicates)
Reads: 82445678 total, 56203 skipped (flags/unmapped)
Fragments: 41466673 total (40869013 tlen-paired, 3655 hash-paired, 384 singletons, 13538 discordant, 580083 orphans, 18298 too large [>5000 bp], 14342326 duplicates)
Reads: 83973611 total, 94173 skipped (flags/unmapped)
Fragments: 42480976 total (40791405 tlen-paired, 2278 hash-paired, 428 singletons, 329883 discordant, 1356982 orphans, 137448 too large [>5000 bp], 14598293 duplicates)