Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/f33e1bd87c9f70985fa4ae76572452/.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-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/659_dvY-N1-BDNA-1_B23L5TMLT4_1/659_dvY-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/f33e1bd87c9f70985fa4ae76572452/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/659_dvY-N1-BDNA-1_B23L5TMLT4_1/659_dvY-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: 659_dvY-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 659_dvY-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.baiThe index file is older than the data file: 659_dvY-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai


The index file is older than the data file: 659_dvY-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: 65989286 total, 52868 skipped (flags/unmapped)
Fragments: 33107790 total (32794190 tlen-paired, 3095 hash-paired, 384 singletons, 12873 discordant, 297248 orphans, 9235 too large [>5000 bp], 12107327 duplicates)
Reads: 70857135 total, 45739 skipped (flags/unmapped)
Fragments: 35550264 total (35229542 tlen-paired, 4127 hash-paired, 401 singletons, 8927 discordant, 307267 orphans, 9268 too large [>5000 bp], 12747956 duplicates)
Reads: 70416440 total, 48634 skipped (flags/unmapped)
Fragments: 35331203 total (34999468 tlen-paired, 4214 hash-paired, 349 singletons, 11073 discordant, 316099 orphans, 10924 too large [>5000 bp], 12946116 duplicates)
Reads: 77303530 total, 81939 skipped (flags/unmapped)
Fragments: 38903196 total (37985893 tlen-paired, 3826 hash-paired, 343 singletons, 180246 discordant, 732888 orphans, 74215 too large [>5000 bp], 14200614 duplicates)