Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_57L-N1-BDNA-1_B23KFG5LT4_1/1136_57L-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_57L-N1-BDNA-1_B23KFG5LT4_1/1136_57L-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/1f1c3fb80edd58336e1f86f2fbe517/.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/44/1f1c3fb80edd58336e1f86f2fbe517/.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_57L-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_57L-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_57L-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_57L-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: 76995054 total, 54742 skipped (flags/unmapped)
Fragments: 38609904 total (38265924 tlen-paired, 3816 hash-paired, 321 singletons, 15122 discordant, 324721 orphans, 22773 too large [>5000 bp], 14986341 duplicates)
Reads: 77207815 total, 51764 skipped (flags/unmapped)
Fragments: 38711213 total (38408555 tlen-paired, 3572 hash-paired, 369 singletons, 11783 discordant, 286934 orphans, 10464 too large [>5000 bp], 14611466 duplicates)
Reads: 72214498 total, 59921 skipped (flags/unmapped)
Fragments: 36208489 total (35907086 tlen-paired, 3276 hash-paired, 420 singletons, 16866 discordant, 280841 orphans, 9430 too large [>5000 bp], 14032748 duplicates)
Reads: 85030016 total, 84036 skipped (flags/unmapped)
Fragments: 42723894 total (41947863 tlen-paired, 3232 hash-paired, 349 singletons, 147477 discordant, 624973 orphans, 61757 too large [>5000 bp], 16615848 duplicates)