File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d8/91158d78e43422099b867853cb6a9b/.command.log
Size
2.3 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FASTQ_ALIGN_STAR:STAR_ALIGNMENT (V4_0001_RNA_0005_23H5VFLT4_s27)
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/d8/91158d78e43422099b867853cb6a9b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/5f3393ce5b6d0acb95fcafe5932efb/V4_0001_RNA_0005_23H5VFLT4_s27_1.fastp.fastq.gz
  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/d8/91158d78e43422099b867853cb6a9b/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/5f3393ce5b6d0acb95fcafe5932efb/V4_0001_RNA_0005_23H5VFLT4_s27_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

	STAR --genomeDir ref_genome.fa.star.idx --readFilesIn input1/V4_0001_RNA_0005_23H5VFLT4_s27_1.fastp.fastq.gz input2/V4_0001_RNA_0005_23H5VFLT4_s27_2.fastp.fastq.gz --runThreadN 24 --outFileNamePrefix V4_0001_RNA_0005_23H5VFLT4_s27. --sjdbGTFfile ref_annot.gtf --outSAMattrRGline ID:V4_0001_RNA_0005_23H5VFLT4_s27 SM:V4_0001_RNA_0005_23H5VFLT4_s27 --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 07:22:41 ..... started STAR run
Jun 08 07:22:41 ..... loading genome
Jun 08 07:23:08 ..... processing annotations GTF
Jun 08 07:23:20 ..... inserting junctions into the genome indices
Jun 08 07:24:53 ..... started mapping
Jun 08 08:16:40 ..... finished mapping
Jun 08 08:16:44 ..... started sorting BAM
Jun 08 08:21:12 ..... finished successfully