Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/c755950acfccb65077f5526bf6884b/.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/d6/c755950acfccb65077f5526bf6884b/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_26N-N1-BDNA-1_A23MHW3LT4_1/1136_26N-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_26N-N1-BDNA-1_A23MHW3LT4_1/1136_26N-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_26N-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1136_26N-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_26N-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_26N-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: 76735193 total, 45904 skipped (flags/unmapped)
Fragments: 38589187 total (38037473 tlen-paired, 4242 hash-paired, 375 singletons, 15373 discordant, 531724 orphans, 21507 too large [>5000 bp], 13074904 duplicates)
Reads: 72175289 total, 51927 skipped (flags/unmapped)
Fragments: 36294661 total (35785119 tlen-paired, 3092 hash-paired, 447 singletons, 17314 discordant, 488689 orphans, 11588 too large [>5000 bp], 12238757 duplicates)
Reads: 77971788 total, 47702 skipped (flags/unmapped)
Fragments: 39205435 total (38678361 tlen-paired, 3222 hash-paired, 555 singletons, 12742 discordant, 510555 orphans, 12163 too large [>5000 bp], 12913287 duplicates)
Reads: 85687520 total, 78216 skipped (flags/unmapped)
Fragments: 43305964 total (41723411 tlen-paired, 2654 hash-paired, 494 singletons, 316133 discordant, 1263272 orphans, 130571 too large [>5000 bp], 14638385 duplicates)