Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_0NF-N1-BDNA-1_A23KFG7LT4_1/1136_0NF-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/07/cbe904fa1cfd5b97cf04d4c56c577c/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_0NF-N1-BDNA-1_A23KFG7LT4_1/1136_0NF-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
  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/07/cbe904fa1cfd5b97cf04d4c56c577c/.command.run
==> 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_0NF-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0NF-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0NF-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0NF-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: 80699429 total, 53528 skipped (flags/unmapped)
Fragments: 40450363 total (40152155 tlen-paired, 2602 hash-paired, 412 singletons, 15295 discordant, 279899 orphans, 12743 too large [>5000 bp], 14909827 duplicates)
Reads: 86288713 total, 45198 skipped (flags/unmapped)
Fragments: 43257451 total (42954620 tlen-paired, 2238 hash-paired, 464 singletons, 10776 discordant, 289353 orphans, 9215 too large [>5000 bp], 15460813 duplicates)
Reads: 85613137 total, 47983 skipped (flags/unmapped)
Fragments: 42922616 total (42588826 tlen-paired, 4433 hash-paired, 398 singletons, 12765 discordant, 316194 orphans, 18257 too large [>5000 bp], 15819564 duplicates)
Reads: 95085538 total, 79435 skipped (flags/unmapped)
Fragments: 47761939 total (46951908 tlen-paired, 1955 hash-paired, 461 singletons, 158915 discordant, 648700 orphans, 65693 too large [>5000 bp], 17620845 duplicates)