Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/75fa7c12b086ed769fe007c18c51b2/.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/b2/75fa7c12b086ed769fe007c18c51b2/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/659_dfA-N1-BDNA-1_B23KFG5LT4_1/659_dfA-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/659_dfA-N1-BDNA-1_B23KFG5LT4_1/659_dfA-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_dfA-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_dfA-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_dfA-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_dfA-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: 84675100 total, 68258 skipped (flags/unmapped)
Fragments: 42466280 total (42091379 tlen-paired, 3504 hash-paired, 544 singletons, 16653 discordant, 354200 orphans, 14513 too large [>5000 bp], 18448970 duplicates)
Reads: 90658342 total, 55437 skipped (flags/unmapped)
Fragments: 45477929 total (45088924 tlen-paired, 3234 hash-paired, 485 singletons, 11508 discordant, 373778 orphans, 10655 too large [>5000 bp], 19370711 duplicates)
Reads: 90454633 total, 59849 skipped (flags/unmapped)
Fragments: 45382475 total (44946450 tlen-paired, 3961 hash-paired, 356 singletons, 14592 discordant, 417116 orphans, 23653 too large [>5000 bp], 19795916 duplicates)
Reads: 100149403 total, 98938 skipped (flags/unmapped)
Fragments: 50373504 total (49284449 tlen-paired, 3729 hash-paired, 416 singletons, 214327 discordant, 870583 orphans, 87228 too large [>5000 bp], 21966667 duplicates)