Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_66D-N1-BDNA-1_B23KFG5LT4_1/1136_66D-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c5/df607362335df0bf1d96557c3f159c/.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/c5/df607362335df0bf1d96557c3f159c/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_66D-N1-BDNA-1_B23KFG5LT4_1/1136_66D-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
==> 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: 1136_66D-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_66D-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_66D-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_66D-N1-BDNA-1_B23KFG5LT4_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: 65354664 total, 50792 skipped (flags/unmapped)
Fragments: 32762043 total (32506439 tlen-paired, 2570 hash-paired, 393 singletons, 15464 discordant, 237177 orphans, 8678 too large [>5000 bp], 13166003 duplicates)
Reads: 68775381 total, 42946 skipped (flags/unmapped)
Fragments: 34474657 total (34226776 tlen-paired, 2180 hash-paired, 362 singletons, 10468 discordant, 234871 orphans, 9177 too large [>5000 bp], 13544474 duplicates)
Reads: 77533772 total, 74080 skipped (flags/unmapped)
Fragments: 38939799 total (38301893 tlen-paired, 2557 hash-paired, 345 singletons, 119049 discordant, 515955 orphans, 48197 too large [>5000 bp], 15749618 duplicates)
Reads: 77254086 total, 46700 skipped (flags/unmapped)
Fragments: 38729284 total (38441698 tlen-paired, 4490 hash-paired, 272 singletons, 15422 discordant, 267402 orphans, 8246 too large [>5000 bp], 15630219 duplicates)