Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_QN-N1-BDNA-1_B23MHTGLT4_1/1029_QN-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/59e6d2bf41dec67db2945a63ac864b/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_QN-N1-BDNA-1_B23MHTGLT4_1/1029_QN-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
  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/8c/59e6d2bf41dec67db2945a63ac864b/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_QN-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_QN-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_QN-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_QN-N1-BDNA-1_B23MHTGLT4_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: 63500731 total, 45877 skipped (flags/unmapped)
Fragments: 31868047 total (31555915 tlen-paired, 2671 hash-paired, 353 singletons, 13049 discordant, 296059 orphans, 7586 too large [>5000 bp], 8737888 duplicates)
Reads: 68278975 total, 39251 skipped (flags/unmapped)
Fragments: 34263624 total (33948677 tlen-paired, 2135 hash-paired, 341 singletons, 9272 discordant, 303199 orphans, 8008 too large [>5000 bp], 9192950 duplicates)
Reads: 67043767 total, 41168 skipped (flags/unmapped)
Fragments: 33648598 total (33308612 tlen-paired, 2449 hash-paired, 320 singletons, 11074 discordant, 326143 orphans, 15933 too large [>5000 bp], 9261837 duplicates)
Reads: 73975788 total, 70778 skipped (flags/unmapped)
Fragments: 37238019 total (36340716 tlen-paired, 2169 hash-paired, 387 singletons, 175366 discordant, 719381 orphans, 74370 too large [>5000 bp], 10248569 duplicates)