Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/05083fc070ccd920b32112ef0261ed/.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/8a/05083fc070ccd920b32112ef0261ed/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_IS4-N1-BDNA-1_B23L5TMLT4_1/1029_IS4-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_IS4-N1-BDNA-1_B23L5TMLT4_1/1029_IS4-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_IS4-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_IS4-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_IS4-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IS4-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: 84173927 total, 63714 skipped (flags/unmapped)
Fragments: 42207579 total (41856592 tlen-paired, 5394 hash-paired, 409 singletons, 16096 discordant, 329088 orphans, 12276 too large [>5000 bp], 14452100 duplicates)
Reads: 90727003 total, 53581 skipped (flags/unmapped)
Fragments: 45492914 total (45138756 tlen-paired, 5084 hash-paired, 506 singletons, 11576 discordant, 336992 orphans, 12546 too large [>5000 bp], 15347607 duplicates)
Reads: 89697888 total, 58331 skipped (flags/unmapped)
Fragments: 44981275 total (44594667 tlen-paired, 5878 hash-paired, 410 singletons, 14063 discordant, 366257 orphans, 21837 too large [>5000 bp], 15472628 duplicates)
Reads: 98856480 total, 96272 skipped (flags/unmapped)
Fragments: 49687162 total (48724117 tlen-paired, 5530 hash-paired, 504 singletons, 186063 discordant, 770948 orphans, 78668 too large [>5000 bp], 17091710 duplicates)