Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_0HE-N1-BDNA-1_A23KFG7LT4_1/1136_0HE-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/b52c94bc45fdc6b57f4004230d6d6d/.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/50/b52c94bc45fdc6b57f4004230d6d6d/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_0HE-N1-BDNA-1_A23KFG7LT4_1/1136_0HE-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
==> 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_0HE-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0HE-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0HE-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0HE-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: 70650105 total, 46060 skipped (flags/unmapped)
Fragments: 35406309 total (35169160 tlen-paired, 2603 hash-paired, 361 singletons, 9105 discordant, 225080 orphans, 8434 too large [>5000 bp], 12778566 duplicates)
Reads: 74650300 total, 39161 skipped (flags/unmapped)
Fragments: 37416097 total (37171553 tlen-paired, 2096 hash-paired, 404 singletons, 6303 discordant, 235741 orphans, 7545 too large [>5000 bp], 13117032 duplicates)
Reads: 82415937 total, 44622 skipped (flags/unmapped)
Fragments: 41310427 total (41020444 tlen-paired, 4807 hash-paired, 302 singletons, 9551 discordant, 275323 orphans, 13043 too large [>5000 bp], 14866682 duplicates)
Reads: 83175960 total, 67996 skipped (flags/unmapped)
Fragments: 41784845 total (41067933 tlen-paired, 2360 hash-paired, 373 singletons, 138994 discordant, 575185 orphans, 56916 too large [>5000 bp], 15054286 duplicates)