File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/d52bf2eb59dbfb9b14cd51fe630be9/.command.log
Size
1.3 KB
Task
NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:GATK4_MARKDUPLICATES (659_x2_T1_TRNA_1_B2372Y3LT4_1)
Attempt

Content

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  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/d52bf2eb59dbfb9b14cd51fe630be9/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/d52bf2eb59dbfb9b14cd51fe630be9/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cc/dbcaa662a03dcaa87a908aba274576/659_x2_T1_TRNA_1_B2372Y3LT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai
==> STAGING COMPLETE (5 inputs)

Using GATK jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar
Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx60620M -XX:-UsePerfData -XX:ParallelGCThreads=2 -jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar MarkDuplicates --INPUT 659_x2_T1_TRNA_1_B2372Y3LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_x2_T1_TRNA_1_B2372Y3LT4_1.md.bam --METRICS_FILE 659_x2_T1_TRNA_1_B2372Y3LT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT