Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bf/7f2cd82f7427f5d01fe8068e721ed3/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_b4v-N1-BDNA-1_A23TNVNLT4_1/659_b4v-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  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/bf/7f2cd82f7427f5d01fe8068e721ed3/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_b4v-N1-BDNA-1_A23TNVNLT4_1/659_b4v-N1-BDNA-1_A23TNVNLT4_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: 659_b4v-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b4v-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b4v-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b4v-N1-BDNA-1_A23TNVNLT4_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: 115091958 total, 80180 skipped (flags/unmapped)
Fragments: 57716016 total (57243807 tlen-paired, 6108 hash-paired, 581 singletons, 14191 discordant, 451329 orphans, 15828 too large [>5000 bp], 24257144 duplicates)
Reads: 124301602 total, 67565 skipped (flags/unmapped)
Fragments: 62354087 total (61838417 tlen-paired, 5198 hash-paired, 640 singletons, 10327 discordant, 499505 orphans, 13004 too large [>5000 bp], 25707149 duplicates)
Reads: 124210995 total, 69060 skipped (flags/unmapped)
Fragments: 62310390 total (61780954 tlen-paired, 4924 hash-paired, 479 singletons, 12999 discordant, 511034 orphans, 16334 too large [>5000 bp], 26473272 duplicates)
Reads: 138616193 total, 129845 skipped (flags/unmapped)
Fragments: 69736560 total (68175645 tlen-paired, 5266 hash-paired, 626 singletons, 319995 discordant, 1235028 orphans, 124441 too large [>5000 bp], 29492404 duplicates)