Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/42/7b04ed668cbd53270059fe3bf126df/.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/42/7b04ed668cbd53270059fe3bf126df/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_ZEX-N1-BDNA-1_A23TY32LT4_1/1241_ZEX-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_ZEX-N1-BDNA-1_A23TY32LT4_1/1241_ZEX-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
==> 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: 1241_ZEX-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1241_ZEX-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1241_ZEX-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_ZEX-N1-BDNA-1_A23TY32LT4_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: 96264520 total, 70381 skipped (flags/unmapped)
Fragments: 48293273 total (47854681 tlen-paired, 4239 hash-paired, 490 singletons, 15730 discordant, 418133 orphans, 13108 too large [>5000 bp], 18622598 duplicates)
Reads: 103775534 total, 59538 skipped (flags/unmapped)
Fragments: 52068892 total (51610740 tlen-paired, 3773 hash-paired, 459 singletons, 11097 discordant, 442823 orphans, 10747 too large [>5000 bp], 19788459 duplicates)
Reads: 113547052 total, 61970 skipped (flags/unmapped)
Fragments: 56970955 total (56456210 tlen-paired, 3502 hash-paired, 308 singletons, 16145 discordant, 494790 orphans, 19135 too large [>5000 bp], 22160800 duplicates)
Reads: 114721122 total, 114775 skipped (flags/unmapped)
Fragments: 57744271 total (56369213 tlen-paired, 2658 hash-paired, 446 singletons, 268059 discordant, 1103895 orphans, 111073 too large [>5000 bp], 22422908 duplicates)