File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/fab35a2fe83c58a0acad7807b5734c/.command.log
Size
1.5 KB
Task
NFCORE_SAREK:SAREK:CRAM_SAMPLE_INTEGRITY:CRAM_QC_RECAL:MOSDEPTH (1029_1H5-N1-BDNA-1_235YY7LT3_1)
Attempt

Content

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  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_1H5-N1-BDNA-1_235YY7LT3_1/1029_1H5-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_1H5-N1-BDNA-1_235YY7LT3_1/1029_1H5-N1-BDNA-1_235YY7LT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/fab35a2fe83c58a0acad7807b5734c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/fab35a2fe83c58a0acad7807b5734c/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/altera_intervals/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed
==> STAGING COMPLETE (6 inputs)

[W::hts_idx_load3] The index file is older than the data file: 1029_1H5-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
ls: *.per-base.d4: No such file or directory
ls: *.quantized.bed.gz: No such file or directory
ls: *.quantized.bed.gz.csi: No such file or directory
ls: *.thresholds.bed.gz: No such file or directory
ls: *.thresholds.bed.gz.csi: No such file or directory