Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/19/1c249e5054915f27cf40cf1321b220/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1047_DI-N1-BDNA-1_B23L5TMLT4_1/1047_DI-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
  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/19/1c249e5054915f27cf40cf1321b220/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1047_DI-N1-BDNA-1_B23L5TMLT4_1/1047_DI-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: 1047_DI-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_DI-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_DI-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_DI-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: 85705496 total, 73378 skipped (flags/unmapped)
Fragments: 43058888 total (42522685 tlen-paired, 4682 hash-paired, 445 singletons, 16367 discordant, 514709 orphans, 14748 too large [>5000 bp], 17450366 duplicates)
Reads: 91777445 total, 62023 skipped (flags/unmapped)
Fragments: 46120761 total (45555779 tlen-paired, 3601 hash-paired, 645 singletons, 11535 discordant, 549201 orphans, 11873 too large [>5000 bp], 18352244 duplicates)
Reads: 91632688 total, 66554 skipped (flags/unmapped)
Fragments: 46045719 total (45475724 tlen-paired, 4826 hash-paired, 440 singletons, 13489 discordant, 551240 orphans, 13188 too large [>5000 bp], 18753272 duplicates)
Reads: 101907580 total, 110029 skipped (flags/unmapped)
Fragments: 51447023 total (49714681 tlen-paired, 5008 hash-paired, 505 singletons, 350039 discordant, 1376790 orphans, 140400 too large [>5000 bp], 20814051 duplicates)