Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/8843b6b9a3b08c0528b8a0c78e69e6/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_3DL-N1-BDNA-1_A23KFG7LT4_1/1136_3DL-N1-BDNA-1_A23KFG7LT4_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/c4/8843b6b9a3b08c0528b8a0c78e69e6/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_3DL-N1-BDNA-1_A23KFG7LT4_1/1136_3DL-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_3DL-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3DL-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3DL-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3DL-N1-BDNA-1_A23KFG7LT4_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: 89872612 total, 64753 skipped (flags/unmapped)
Fragments: 45142577 total (44619719 tlen-paired, 4574 hash-paired, 492 singletons, 16663 discordant, 501129 orphans, 12163 too large [>5000 bp], 17070278 duplicates)
Reads: 94675028 total, 54415 skipped (flags/unmapped)
Fragments: 47557367 total (47024344 tlen-paired, 2923 hash-paired, 557 singletons, 11589 discordant, 517954 orphans, 12195 too large [>5000 bp], 17550733 duplicates)
Reads: 104588403 total, 56559 skipped (flags/unmapped)
Fragments: 52540593 total (51921253 tlen-paired, 3682 hash-paired, 379 singletons, 16446 discordant, 598833 orphans, 24935 too large [>5000 bp], 19924957 duplicates)
Reads: 106354963 total, 93140 skipped (flags/unmapped)
Fragments: 53671205 total (51980855 tlen-paired, 4038 hash-paired, 500 singletons, 332031 discordant, 1353781 orphans, 136847 too large [>5000 bp], 20260507 duplicates)