Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1136_36J-N1-BDNA-1_B23L5TMLT4_1/1136_36J-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/14a6740944251bdd041136f3e85f4d/.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/83/14a6740944251bdd041136f3e85f4d/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1136_36J-N1-BDNA-1_B23L5TMLT4_1/1136_36J-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: 1136_36J-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_36J-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_36J-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_36J-N1-BDNA-1_B23L5TMLT4_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: 102084802 total, 69242 skipped (flags/unmapped)
Fragments: 51198638 total (50766932 tlen-paired, 5747 hash-paired, 682 singletons, 15643 discordant, 409634 orphans, 14300 too large [>5000 bp], 18807216 duplicates)
Reads: 95748593 total, 81449 skipped (flags/unmapped)
Fragments: 48023778 total (47588476 tlen-paired, 5831 hash-paired, 508 singletons, 22521 discordant, 406442 orphans, 13269 too large [>5000 bp], 17840373 duplicates)
Reads: 101098248 total, 73792 skipped (flags/unmapped)
Fragments: 50710851 total (50231853 tlen-paired, 9076 hash-paired, 554 singletons, 19262 discordant, 450106 orphans, 26707 too large [>5000 bp], 19018014 duplicates)
Reads: 112041372 total, 122495 skipped (flags/unmapped)
Fragments: 56326941 total (55180541 tlen-paired, 4806 hash-paired, 586 singletons, 219623 discordant, 921385 orphans, 93483 too large [>5000 bp], 21129948 duplicates)