File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/eebd450e195fea054a4ee102f2b7c7/.command.log
Size
2.2 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FASTQ_ALIGN_STAR:STAR_ALIGNMENT (rna_s1200_S21)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/2a1aeee1b10b93bd5000d3db51bcdf/rna_s1200_S21_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/eebd450e195fea054a4ee102f2b7c7/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_annot.gtf
  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/8a/eebd450e195fea054a4ee102f2b7c7/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/2a1aeee1b10b93bd5000d3db51bcdf/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 28 16:33:14 ..... started STAR run
May 28 16:33:14 ..... loading genome
May 28 16:33:29 ..... processing annotations GTF
May 28 16:33:37 ..... inserting junctions into the genome indices
May 28 16:34:38 ..... started mapping
May 28 16:36:09 ..... finished mapping
May 28 16:36:10 ..... started sorting BAM
May 28 16:36:18 ..... finished successfully