File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/4c2e7e617359a2c6f2b5010c9c6a5c/.command.log
Size
2.2 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FASTQ_ALIGN_STAR:STAR_ALIGNMENT (rna_s1200_S21)
Attempt

Content

View in new tab 
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/06c5423b1f45051d87ad27845d475f/rna_s1200_S21_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/c1/4c2e7e617359a2c6f2b5010c9c6a5c/.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/c1/4c2e7e617359a2c6f2b5010c9c6a5c/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/06c5423b1f45051d87ad27845d475f/rna_s1200_S21_1.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

	STAR --genomeDir ref_genome.fa.star.idx --readFilesIn input1/rna_s1200_S21_1.fastp.fastq.gz input2/rna_s1200_S21_2.fastp.fastq.gz --runThreadN 24 --outFileNamePrefix rna_s1200_S21. --sjdbGTFfile ref_annot.gtf --outSAMattrRGline ID:rna_s1200_S21 SM:rna_s1200_S21 --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
May 27 21:56:12 ..... started STAR run
May 27 21:56:12 ..... loading genome
May 27 21:56:25 ..... processing annotations GTF
May 27 21:56:33 ..... inserting junctions into the genome indices
May 27 21:57:45 ..... started mapping
May 27 21:58:53 ..... finished mapping
May 27 21:58:55 ..... started sorting BAM
May 27 21:59:03 ..... finished successfully