File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/993d7220d8446b61d7f0e428187633/.command.log
Size
2.3 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FASTQ_ALIGN_STAR:STAR_ALIGNMENT (A673_FFPE_RNA_0001_B23LG7FLT4_2)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/380c8a29d02bdaad5dfdf4322cdd43/A673_FFPE_RNA_0001_B23LG7FLT4_2_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/380c8a29d02bdaad5dfdf4322cdd43/A673_FFPE_RNA_0001_B23LG7FLT4_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/a8/993d7220d8446b61d7f0e428187633/.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/a8/993d7220d8446b61d7f0e428187633/.command.run
==> STAGING COMPLETE (6 inputs)

	STAR --genomeDir ref_genome.fa.star.idx --readFilesIn input1/A673_FFPE_RNA_0001_B23LG7FLT4_2_1.fastp.fastq.gz input2/A673_FFPE_RNA_0001_B23LG7FLT4_2_2.fastp.fastq.gz --runThreadN 24 --outFileNamePrefix A673_FFPE_RNA_0001_B23LG7FLT4_2. --sjdbGTFfile ref_annot.gtf --outSAMattrRGline ID:A673_FFPE_RNA_0001_B23LG7FLT4_2 SM:A673_FFPE_RNA_0001_B23LG7FLT4_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 08 07:34:13 ..... started STAR run
Jun 08 07:34:13 ..... loading genome
Jun 08 07:34:38 ..... processing annotations GTF
Jun 08 07:34:49 ..... inserting junctions into the genome indices
Jun 08 07:36:24 ..... started mapping
Jun 08 08:20:41 ..... finished mapping
Jun 08 08:20:45 ..... started sorting BAM
Jun 08 08:25:06 ..... finished successfully