Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_8w-N1-BDNA-1_A23TNVNLT4_1/659_8w-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/fadcf9e58dfdc45d32f59aa2e21d34/.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/c8/fadcf9e58dfdc45d32f59aa2e21d34/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_8w-N1-BDNA-1_A23TNVNLT4_1/659_8w-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 659_8w-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
The index file is older than the data file: 659_8w-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_8w-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_8w-N1-BDNA-1_A23TNVNLT4_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: 85255510 total, 58369 skipped (flags/unmapped)
Fragments: 42734760 total (42425057 tlen-paired, 3506 hash-paired, 465 singletons, 13956 discordant, 291776 orphans, 9931 too large [>5000 bp], 15572023 duplicates)
Reads: 92352899 total, 47857 skipped (flags/unmapped)
Fragments: 46297460 total (45977792 tlen-paired, 3217 hash-paired, 418 singletons, 9795 discordant, 306238 orphans, 8389 too large [>5000 bp], 16582564 duplicates)
Reads: 91812479 total, 51977 skipped (flags/unmapped)
Fragments: 46030512 total (45675393 tlen-paired, 4077 hash-paired, 347 singletons, 12622 discordant, 338073 orphans, 18949 too large [>5000 bp], 16929710 duplicates)
Reads: 102060194 total, 96446 skipped (flags/unmapped)
Fragments: 51267224 total (50371101 tlen-paired, 4996 hash-paired, 454 singletons, 177371 discordant, 713302 orphans, 71528 too large [>5000 bp], 18843743 duplicates)