Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_MKM-N1-BDNA-1_B23L5TMLT4_1/1029_MKM-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_MKM-N1-BDNA-1_B23L5TMLT4_1/1029_MKM-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/37baa8b28ee7b2c74e5111999865ad/.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/a1/37baa8b28ee7b2c74e5111999865ad/.command.run
==> 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_MKM-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_MKM-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_MKM-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_MKM-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: 81212864 total, 59905 skipped (flags/unmapped)
Fragments: 40673081 total (40438178 tlen-paired, 4906 hash-paired, 527 singletons, 7816 discordant, 221654 orphans, 14489 too large [>5000 bp], 14179976 duplicates)
Reads: 91412262 total, 52151 skipped (flags/unmapped)
Fragments: 45799124 total (45528588 tlen-paired, 4733 hash-paired, 642 singletons, 6406 discordant, 258755 orphans, 10630 too large [>5000 bp], 15766636 duplicates)
Reads: 87100599 total, 52004 skipped (flags/unmapped)
Fragments: 43640152 total (43354677 tlen-paired, 10292 hash-paired, 426 singletons, 7390 discordant, 267367 orphans, 18042 too large [>5000 bp], 15153248 duplicates)
Reads: 95207245 total, 93631 skipped (flags/unmapped)
Fragments: 47794690 total (47058286 tlen-paired, 4083 hash-paired, 554 singletons, 147379 discordant, 584388 orphans, 54588 too large [>5000 bp], 16576288 duplicates)