Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/098f1f77d6e94b031b2b4e73a91045/.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/7c/098f1f77d6e94b031b2b4e73a91045/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1047_HK-N1-BDNA-1_B23L5TMLT4_1/1047_HK-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/1047_HK-N1-BDNA-1_B23L5TMLT4_1/1047_HK-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1047_HK-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1047_HK-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1047_HK-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1047_HK-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: 58046678 total, 44393 skipped (flags/unmapped)
Fragments: 29123260 total (28849728 tlen-paired, 2872 hash-paired, 331 singletons, 9959 discordant, 260370 orphans, 8233 too large [>5000 bp], 10177669 duplicates)
Reads: 62398067 total, 38311 skipped (flags/unmapped)
Fragments: 31307875 total (31026073 tlen-paired, 2865 hash-paired, 380 singletons, 7233 discordant, 271324 orphans, 7855 too large [>5000 bp], 10691935 duplicates)
Reads: 61893121 total, 39615 skipped (flags/unmapped)
Fragments: 31059554 total (30750422 tlen-paired, 5183 hash-paired, 288 singletons, 9029 discordant, 294632 orphans, 14659 too large [>5000 bp], 10857844 duplicates)
Reads: 68556998 total, 67171 skipped (flags/unmapped)
Fragments: 34505535 total (33680621 tlen-paired, 2656 hash-paired, 321 singletons, 163321 discordant, 658616 orphans, 68847 too large [>5000 bp], 12043616 duplicates)