Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/fec11de045cccc0d6c3b786f4f797e/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_BIBA-N1-BDNA-1_B23L5TMLT4_1/1029_BIBA-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  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/0f/fec11de045cccc0d6c3b786f4f797e/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_BIBA-N1-BDNA-1_B23L5TMLT4_1/1029_BIBA-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
==> 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: 1029_BIBA-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BIBA-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BIBA-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_BIBA-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: 124052388 total, 97440 skipped (flags/unmapped)
Fragments: 62298267 total (61583973 tlen-paired, 6049 hash-paired, 732 singletons, 28567 discordant, 678946 orphans, 19046 too large [>5000 bp], 24236727 duplicates)
Reads: 130579594 total, 89135 skipped (flags/unmapped)
Fragments: 65580399 total (64813885 tlen-paired, 7157 hash-paired, 627 singletons, 24220 discordant, 734510 orphans, 32399 too large [>5000 bp], 25662420 duplicates)
Reads: 132682478 total, 83395 skipped (flags/unmapped)
Fragments: 66630417 total (65902440 tlen-paired, 5672 hash-paired, 814 singletons, 20772 discordant, 700719 orphans, 19891 too large [>5000 bp], 25482723 duplicates)
Reads: 145824138 total, 143838 skipped (flags/unmapped)
Fragments: 73508550 total (71399095 tlen-paired, 6362 hash-paired, 743 singletons, 418205 discordant, 1684145 orphans, 174044 too large [>5000 bp], 28672228 duplicates)