Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/934ec607b869f8381f1b76fba57305/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_0YS-N1-BDNA-1_A23MHW3LT4_1/1136_0YS-N1-BDNA-1_A23MHW3LT4_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/cb/934ec607b869f8381f1b76fba57305/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_0YS-N1-BDNA-1_A23MHW3LT4_1/1136_0YS-N1-BDNA-1_A23MHW3LT4_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: 1136_0YS-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_0YS-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_0YS-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_0YS-N1-BDNA-1_A23MHW3LT4_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: 76561246 total, 64412 skipped (flags/unmapped)
Fragments: 38472232 total (37978467 tlen-paired, 4051 hash-paired, 427 singletons, 15850 discordant, 473437 orphans, 13117 too large [>5000 bp], 12642253 duplicates)
Reads: 80449828 total, 52280 skipped (flags/unmapped)
Fragments: 40429355 total (39932263 tlen-paired, 2581 hash-paired, 433 singletons, 10615 discordant, 483463 orphans, 11367 too large [>5000 bp], 13024843 duplicates)
Reads: 87848590 total, 58761 skipped (flags/unmapped)
Fragments: 44152579 total (43583926 tlen-paired, 5022 hash-paired, 474 singletons, 15916 discordant, 547241 orphans, 16193 too large [>5000 bp], 14548284 duplicates)
Reads: 88886741 total, 95908 skipped (flags/unmapped)
Fragments: 44896087 total (43332769 tlen-paired, 2567 hash-paired, 522 singletons, 302928 discordant, 1257301 orphans, 128241 too large [>5000 bp], 14711850 duplicates)