Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_1ZL-N1-BDNA-1_A23MHW3LT4_1/1136_1ZL-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/740f22db652da741b4e078b413c95e/.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/cb/740f22db652da741b4e078b413c95e/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_1ZL-N1-BDNA-1_A23MHW3LT4_1/1136_1ZL-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
==> 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_1ZL-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_1ZL-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_1ZL-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_1ZL-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: 77063922 total, 54802 skipped (flags/unmapped)
Fragments: 38690880 total (38274532 tlen-paired, 2566 hash-paired, 435 singletons, 14994 discordant, 398353 orphans, 13074 too large [>5000 bp], 13353988 duplicates)
Reads: 82148559 total, 48468 skipped (flags/unmapped)
Fragments: 41243088 total (40820148 tlen-paired, 3077 hash-paired, 510 singletons, 10342 discordant, 409011 orphans, 11718 too large [>5000 bp], 13890789 duplicates)
Reads: 89975514 total, 52581 skipped (flags/unmapped)
Fragments: 45179433 total (44700062 tlen-paired, 4404 hash-paired, 432 singletons, 14964 discordant, 459571 orphans, 12035 too large [>5000 bp], 15651541 duplicates)
Reads: 90825049 total, 82736 skipped (flags/unmapped)
Fragments: 45782862 total (44499219 tlen-paired, 2443 hash-paired, 458 singletons, 249319 discordant, 1031423 orphans, 104235 too large [>5000 bp], 15829795 duplicates)