Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/8ea645b55298fdf90497b75a8e531a/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_8FW-N1-BDNA-1_A23TNVNLT4_1/1241_8FW-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_8FW-N1-BDNA-1_A23TNVNLT4_1/1241_8FW-N1-BDNA-1_A23TNVNLT4_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/ff/8ea645b55298fdf90497b75a8e531a/.command.run
==> 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: 1241_8FW-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_8FW-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_8FW-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1241_8FW-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: 93746244 total, 64748 skipped (flags/unmapped)
Fragments: 46988507 total (46652578 tlen-paired, 4183 hash-paired, 528 singletons, 13678 discordant, 317540 orphans, 11275 too large [>5000 bp], 18153788 duplicates)
Reads: 100534492 total, 52865 skipped (flags/unmapped)
Fragments: 50401226 total (50049254 tlen-paired, 3146 hash-paired, 593 singletons, 9609 discordant, 338624 orphans, 9196 too large [>5000 bp], 19146398 duplicates)
Reads: 110539969 total, 57999 skipped (flags/unmapped)
Fragments: 55414500 total (55007298 tlen-paired, 5232 hash-paired, 414 singletons, 14484 discordant, 387072 orphans, 20228 too large [>5000 bp], 21476866 duplicates)
Reads: 111827894 total, 102605 skipped (flags/unmapped)
Fragments: 56192684 total (55172194 tlen-paired, 4174 hash-paired, 507 singletons, 199737 discordant, 816072 orphans, 78250 too large [>5000 bp], 21778150 duplicates)