Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_HSC-N1-BDNA-1_B23L5TMLT4_1/1029_HSC-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_HSC-N1-BDNA-1_B23L5TMLT4_1/1029_HSC-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/8bcca7b4c32945592196ab486ade26/.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/7a/8bcca7b4c32945592196ab486ade26/.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_HSC-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai[W::hts_idx_load3] The index file is older than the data file: 1029_HSC-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_HSC-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_HSC-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: 112443969 total, 84921 skipped (flags/unmapped)
Fragments: 56340875 total (55962855 tlen-paired, 6054 hash-paired, 750 singletons, 13490 discordant, 357726 orphans, 17887 too large [>5000 bp], 21352555 duplicates)
Reads: 123304366 total, 71947 skipped (flags/unmapped)
Fragments: 61807376 total (61382745 tlen-paired, 4822 hash-paired, 763 singletons, 10464 discordant, 408582 orphans, 13506 too large [>5000 bp], 22968543 duplicates)
Reads: 120079887 total, 73879 skipped (flags/unmapped)
Fragments: 60186054 total (59731633 tlen-paired, 5008 hash-paired, 575 singletons, 11975 discordant, 436863 orphans, 35669 too large [>5000 bp], 22745929 duplicates)
Reads: 132223926 total, 134646 skipped (flags/unmapped)
Fragments: 66422919 total (65244477 tlen-paired, 5122 hash-paired, 674 singletons, 233342 discordant, 939304 orphans, 91710 too large [>5000 bp], 25067643 duplicates)