Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/d03c6a727fa3d5e6701fd88a9ab939/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/659_dXa-N1-BDNA-1_B23KFG5LT4_1/659_dXa-N1-BDNA-1_B23KFG5LT4_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/3a/d03c6a727fa3d5e6701fd88a9ab939/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/659_dXa-N1-BDNA-1_B23KFG5LT4_1/659_dXa-N1-BDNA-1_B23KFG5LT4_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: 659_dXa-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_dXa-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_dXa-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_dXa-N1-BDNA-1_B23KFG5LT4_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: 70874272 total, 59650 skipped (flags/unmapped)
Fragments: 35538999 total (35239395 tlen-paired, 3176 hash-paired, 359 singletons, 17046 discordant, 279023 orphans, 8003 too large [>5000 bp], 14897799 duplicates)
Reads: 77649081 total, 52570 skipped (flags/unmapped)
Fragments: 38933968 total (38625595 tlen-paired, 3109 hash-paired, 433 singletons, 11725 discordant, 293106 orphans, 11057 too large [>5000 bp], 15901805 duplicates)
Reads: 77949170 total, 51870 skipped (flags/unmapped)
Fragments: 39087431 total (38759898 tlen-paired, 2910 hash-paired, 295 singletons, 15079 discordant, 309249 orphans, 15991 too large [>5000 bp], 16500985 duplicates)
Reads: 85838624 total, 83263 skipped (flags/unmapped)
Fragments: 43135168 total (42343503 tlen-paired, 1799 hash-paired, 339 singletons, 154245 discordant, 635282 orphans, 60323 too large [>5000 bp], 18254120 duplicates)