Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1136_6SP-N1-BDNA-1_B23L5TMLT4_1/1136_6SP-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/1d09b07b6cab00759401eebfc1dd1b/.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/a4/1d09b07b6cab00759401eebfc1dd1b/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1136_6SP-N1-BDNA-1_B23L5TMLT4_1/1136_6SP-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_6SP-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] Count mode: frac
The index file is older than the data file: 1136_6SP-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6SP-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6SP-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: 95213123 total, 69894 skipped (flags/unmapped)
Fragments: 47791549 total (47299246 tlen-paired, 5565 hash-paired, 654 singletons, 11763 discordant, 474321 orphans, 17553 too large [>5000 bp], 18676933 duplicates)
Reads: 88569901 total, 77693 skipped (flags/unmapped)
Fragments: 44458800 total (43986541 tlen-paired, 4049 hash-paired, 599 singletons, 16626 discordant, 450985 orphans, 13096 too large [>5000 bp], 17643115 duplicates)
Reads: 105004887 total, 117654 skipped (flags/unmapped)
Fragments: 52919879 total (51433881 tlen-paired, 4758 hash-paired, 541 singletons, 288801 discordant, 1191898 orphans, 119957 too large [>5000 bp], 20986024 duplicates)
Reads: 103981510 total, 72185 skipped (flags/unmapped)
Fragments: 52203447 total (51654515 tlen-paired, 4963 hash-paired, 501 singletons, 16218 discordant, 527250 orphans, 15091 too large [>5000 bp], 20793854 duplicates)