File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/15f7d615690c5e02da7a08acc5f63e/.command.log
Size
2.3 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FASTQ_ALIGN_STAR:STAR_ALIGNMENT (FFPE_V4_0001_RNA_0003_B23MHV2LT4_2)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/04ddd470449bbda0ae0c0be66e0f90/FFPE_V4_0001_RNA_0003_B23MHV2LT4_2_2.fastp.fastq.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_annot.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/15f7d615690c5e02da7a08acc5f63e/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/15f7d615690c5e02da7a08acc5f63e/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/04ddd470449bbda0ae0c0be66e0f90/FFPE_V4_0001_RNA_0003_B23MHV2LT4_2_1.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

	STAR --genomeDir ref_genome.fa.star.idx --readFilesIn input1/FFPE_V4_0001_RNA_0003_B23MHV2LT4_2_1.fastp.fastq.gz input2/FFPE_V4_0001_RNA_0003_B23MHV2LT4_2_2.fastp.fastq.gz --runThreadN 24 --outFileNamePrefix FFPE_V4_0001_RNA_0003_B23MHV2LT4_2. --sjdbGTFfile ref_annot.gtf --outSAMattrRGline ID:FFPE_V4_0001_RNA_0003_B23MHV2LT4_2 SM:FFPE_V4_0001_RNA_0003_B23MHV2LT4_2 --twopassMode None --chimSegmentMin 12 --chimJunctionOverhangMin 5 --chimMultimapNmax 50 --chimScoreJunctionNonGTAG -4 --chimScoreSeparation 1 --alignIntronMax 140000 --outReadsUnmapped None --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSAMunmapped Within --chimOutJunctionFormat 1 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignSJstitchMismatchNmax 5 -1 5 5 --chimMultimapScoreRange 3 --chimNonchimScoreDropMin 10 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --alignInsertionFlush Right --alignSplicedMateMapLmin 30 --alignSplicedMateMapLminOverLmate 0.5 --quantMode GeneCounts --runRNGseed 1 --chimOutType Junctions WithinBAM --limitBAMsortRAM 38654705664
	STAR version: 2.7.10a   compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source
Jun 04 20:27:45 ..... started STAR run
Jun 04 20:27:45 ..... loading genome
Jun 04 20:28:02 ..... processing annotations GTF
Jun 04 20:28:10 ..... inserting junctions into the genome indices
Jun 04 20:29:16 ..... started mapping
Jun 04 21:06:23 ..... finished mapping
Jun 04 21:06:26 ..... started sorting BAM
Jun 04 21:10:31 ..... finished successfully