Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/77b00c1de092e7267df86f625335e1/.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/5c/77b00c1de092e7267df86f625335e1/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_BFGZ-N1-BDNA-1_B23L5TMLT4_1/1029_BFGZ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_BFGZ-N1-BDNA-1_B23L5TMLT4_1/1029_BFGZ-N1-BDNA-1_B23L5TMLT4_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: 1029_BFGZ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BFGZ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BFGZ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BFGZ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
Deduplicated 94 probes with identical coordinates
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
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: 82006893 total, 59911 skipped (flags/unmapped)
Fragments: 41181416 total (40726401 tlen-paired, 3936 hash-paired, 575 singletons, 16989 discordant, 433515 orphans, 9120 too large [>5000 bp], 14702695 duplicates)
Reads: 86366912 total, 54064 skipped (flags/unmapped)
Fragments: 43374556 total (42871497 tlen-paired, 4830 hash-paired, 451 singletons, 15021 discordant, 482757 orphans, 23472 too large [>5000 bp], 15510035 duplicates)
Reads: 87989545 total, 53599 skipped (flags/unmapped)
Fragments: 44181459 total (43713219 tlen-paired, 3639 hash-paired, 631 singletons, 12565 discordant, 451405 orphans, 12532 too large [>5000 bp], 15470054 duplicates)
Reads: 96202141 total, 99816 skipped (flags/unmapped)
Fragments: 48483621 total (47116206 tlen-paired, 3276 hash-paired, 550 singletons, 271058 discordant, 1092531 orphans, 114082 too large [>5000 bp], 17241889 duplicates)