Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_1DO-N1-BDNA-1_A23KFG7LT4_1/1136_1DO-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dc/65753840041bcfc6362b4b97243371/.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/dc/65753840041bcfc6362b4b97243371/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_1DO-N1-BDNA-1_A23KFG7LT4_1/1136_1DO-N1-BDNA-1_A23KFG7LT4_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_1DO-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_1DO-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_1DO-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_1DO-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: 61428894 total, 43035 skipped (flags/unmapped)
Fragments: 30785937 total (30569061 tlen-paired, 2218 hash-paired, 258 singletons, 9971 discordant, 204429 orphans, 9336 too large [>5000 bp], 10074780 duplicates)
Reads: 66188499 total, 36616 skipped (flags/unmapped)
Fragments: 33175800 total (32950496 tlen-paired, 2623 hash-paired, 347 singletons, 6946 discordant, 215388 orphans, 8009 too large [>5000 bp], 10566788 duplicates)
Reads: 71996523 total, 66235 skipped (flags/unmapped)
Fragments: 36169641 total (35541564 tlen-paired, 2403 hash-paired, 341 singletons, 119878 discordant, 505455 orphans, 48401 too large [>5000 bp], 11860958 duplicates)
Reads: 71597854 total, 39069 skipped (flags/unmapped)
Fragments: 35891243 total (35626149 tlen-paired, 2685 hash-paired, 277 singletons, 9978 discordant, 252154 orphans, 14365 too large [>5000 bp], 11763633 duplicates)