File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/bc8f89d3fffa34dab01f8a8a1ff315/.command.log
Size
2.2 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FASTQ_ALIGN_STAR:STAR_ALIGNMENT (rna_s1221_S42)
Attempt

Content

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  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/28/bc8f89d3fffa34dab01f8a8a1ff315/.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/28/bc8f89d3fffa34dab01f8a8a1ff315/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/55dee359292f4c00249a6d03f86d51/rna_s1221_S42_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/55dee359292f4c00249a6d03f86d51/rna_s1221_S42_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

	STAR --genomeDir ref_genome.fa.star.idx --readFilesIn input1/rna_s1221_S42_1.fastp.fastq.gz input2/rna_s1221_S42_2.fastp.fastq.gz --runThreadN 24 --outFileNamePrefix rna_s1221_S42. --sjdbGTFfile ref_annot.gtf --outSAMattrRGline ID:rna_s1221_S42 SM:rna_s1221_S42 --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 02:10:37 ..... started STAR run
Jun 04 02:10:37 ..... loading genome
Jun 04 02:10:51 ..... processing annotations GTF
Jun 04 02:11:00 ..... inserting junctions into the genome indices
Jun 04 02:11:59 ..... started mapping
Jun 04 02:13:19 ..... finished mapping
Jun 04 02:13:20 ..... started sorting BAM
Jun 04 02:13:29 ..... finished successfully