File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d0/d94de4c80d2c3bd45e44d7365ccaf8/.command.log
Size
2.3 KB
Task
MIX_BAMS (NA18508_x_NA18522_FF_5)
Attempt

Content

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  Downloading: s3://natera-platform-sandbox/pipeline-outputs/flowcell-runs/20260210_LH00519_0056_A23K2N2LT4/1076-add-custom-fastq-sample-merging_afd6c9_260212144006/bams/3599996111_r8_L48.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d0/d94de4c80d2c3bd45e44d7365ccaf8/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/flowcell-runs/20260210_LH00519_0056_A23K2N2LT4/1076-add-custom-fastq-sample-merging_afd6c9_260212144006/bams/3599996112_r8_L48.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/flowcell-runs/20260210_LH00519_0056_A23K2N2LT4/1076-add-custom-fastq-sample-merging_afd6c9_260212144006/bams/3599996112_r8_L48.bam.bai
  Downloading: s3://natera-platform-sandbox/projects/lcvs/bed-files/xgen-exome-research-panel-v2-targets-hg38.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d0/d94de4c80d2c3bd45e44d7365ccaf8/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/flowcell-runs/20260210_LH00519_0056_A23K2N2LT4/1076-add-custom-fastq-sample-merging_afd6c9_260212144006/bams/3599996111_r8_L48.bam.bai
==> STAGING COMPLETE (7 inputs)

[MIX_BAMS:NA18508_x_NA18522_FF_5] BED: 197769 intervals, sampled 2019 covering 359155 bp
[W::hts_idx_load3] The index file is older than the data file: 3599996111_r8_L48.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 3599996112_r8_L48.bam.bai
[MIX_BAMS:NA18508_x_NA18522_FF_5] maternal: 3599996111_r8_L48.bam reads=174478833 on_target_cov=201.0406x
[MIX_BAMS:NA18508_x_NA18522_FF_5] fetal:    3599996112_r8_L48.bam reads=109849900 on_target_cov=128.1235x
[MIX_BAMS:NA18508_x_NA18522_FF_5] effective target=200.0000x  fractions: mat=0.9451 fet=0.0780  status=OK
[MIX_BAMS:NA18508_x_NA18522_FF_5] after subsample: mat=164900794/174478833 fet=8571382/109849900
[bam_translate] PG tag "MarkDuplicates" on read "LH00519:56:23K2N2LT4:4:2284:35465:14181" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "MarkDuplicates" on read "LH00519:56:23K2N2LT4:4:1266:39155:14237" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[MIX_BAMS:NA18508_x_NA18522_FF_5] mixture:  NA18508_x_NA18522_FF_5.mix.bam reads=173472176 on_target_cov=199.9710x observed_ff=0.0494