Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/dfcfa11c568f24d60a684595b12637/.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/9b/dfcfa11c568f24d60a684595b12637/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/659_er7-N1-BDNA-1_B23L5TMLT4_1/659_er7-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/659_er7-N1-BDNA-1_B23L5TMLT4_1/659_er7-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: 659_er7-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] Count mode: frac
The index file is older than the data file: 659_er7-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_er7-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_er7-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: 66738996 total, 51765 skipped (flags/unmapped)
Fragments: 33497136 total (33160680 tlen-paired, 3303 hash-paired, 369 singletons, 11424 discordant, 321360 orphans, 7344 too large [>5000 bp], 11990729 duplicates)
Reads: 72324536 total, 46036 skipped (flags/unmapped)
Fragments: 36299432 total (35945778 tlen-paired, 3729 hash-paired, 445 singletons, 8543 discordant, 340937 orphans, 10509 too large [>5000 bp], 12773223 duplicates)
Reads: 71096478 total, 45180 skipped (flags/unmapped)
Fragments: 35687131 total (35310579 tlen-paired, 2899 hash-paired, 363 singletons, 10069 discordant, 363221 orphans, 20310 too large [>5000 bp], 12818658 duplicates)
Reads: 78650781 total, 79698 skipped (flags/unmapped)
Fragments: 39616275 total (38572933 tlen-paired, 3343 hash-paired, 384 singletons, 207576 discordant, 832039 orphans, 85478 too large [>5000 bp], 14189356 duplicates)