Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/659_eOm-N1-BDNA-1_B23L5TMLT4_1/659_eOm-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/aa/2e05dac7981ab3123ec1b06d8314f6/.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/aa/2e05dac7981ab3123ec1b06d8314f6/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/659_eOm-N1-BDNA-1_B23L5TMLT4_1/659_eOm-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: 659_eOm-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eOm-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eOm-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eOm-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: 95059579 total, 75143 skipped (flags/unmapped)
Fragments: 47685042 total (47246678 tlen-paired, 6000 hash-paired, 562 singletons, 16886 discordant, 414916 orphans, 14915 too large [>5000 bp], 19097707 duplicates)
Reads: 101535698 total, 59816 skipped (flags/unmapped)
Fragments: 50944504 total (50490468 tlen-paired, 4969 hash-paired, 592 singletons, 11271 discordant, 437204 orphans, 12335 too large [>5000 bp], 20132961 duplicates)
Reads: 100717720 total, 66010 skipped (flags/unmapped)
Fragments: 50534948 total (50048898 tlen-paired, 5576 hash-paired, 486 singletons, 13602 discordant, 466386 orphans, 24343 too large [>5000 bp], 20336186 duplicates)
Reads: 111942942 total, 107959 skipped (flags/unmapped)
Fragments: 56336709 total (55014928 tlen-paired, 3989 hash-paired, 558 singletons, 263875 discordant, 1053359 orphans, 107741 too large [>5000 bp], 22576063 duplicates)