Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/b103d4f6f8d574fdd225274aad7e12/.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/7a/b103d4f6f8d574fdd225274aad7e12/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_3JH-N1-BDNA-1_A23H3NYLT3_1/1136_3JH-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_3JH-N1-BDNA-1_A23H3NYLT3_1/1136_3JH-N1-BDNA-1_A23H3NYLT3_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_3JH-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3JH-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3JH-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3JH-N1-BDNA-1_A23H3NYLT3_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: 57802307 total, 50050 skipped (flags/unmapped)
Fragments: 29044981 total (28672958 tlen-paired, 8459 hash-paired, 4760 singletons, 6085 discordant, 352719 orphans, 9887 too large [>5000 bp], 3807471 duplicates)
Reads: 58556786 total, 53517 skipped (flags/unmapped)
Fragments: 29415614 total (29057436 tlen-paired, 7819 hash-paired, 4752 singletons, 6938 discordant, 338669 orphans, 7731 too large [>5000 bp], 3873649 duplicates)
Reads: 64164398 total, 48122 skipped (flags/unmapped)
Fragments: 32247454 total (31838299 tlen-paired, 8049 hash-paired, 5108 singletons, 5520 discordant, 390478 orphans, 8477 too large [>5000 bp], 4183484 duplicates)
Reads: 64339966 total, 77332 skipped (flags/unmapped)
Fragments: 32527379 total (31304361 tlen-paired, 7339 hash-paired, 5261 singletons, 241577 discordant, 968841 orphans, 90989 too large [>5000 bp], 4193230 duplicates)