File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/3cc447fd28e50c8a55732a08848a6a/.command.log
Size
2.3 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FASTQ_ALIGN_STAR:STAR_ALIGNMENT (tih_rna_sample_00403_23H5VFLT4_s29)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cc/971fba390509ad6db4d98175063a14/tih_rna_sample_00403_23H5VFLT4_s29_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/a5/3cc447fd28e50c8a55732a08848a6a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cc/971fba390509ad6db4d98175063a14/tih_rna_sample_00403_23H5VFLT4_s29_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/a5/3cc447fd28e50c8a55732a08848a6a/.command.run
==> STAGING COMPLETE (6 inputs)

	STAR --genomeDir ref_genome.fa.star.idx --readFilesIn input1/tih_rna_sample_00403_23H5VFLT4_s29_1.fastp.fastq.gz input2/tih_rna_sample_00403_23H5VFLT4_s29_2.fastp.fastq.gz --runThreadN 24 --outFileNamePrefix tih_rna_sample_00403_23H5VFLT4_s29. --sjdbGTFfile ref_annot.gtf --outSAMattrRGline ID:tih_rna_sample_00403_23H5VFLT4_s29 SM:tih_rna_sample_00403_23H5VFLT4_s29 --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 07:16:50 ..... started STAR run
Jun 08 07:16:50 ..... loading genome
Jun 08 07:17:17 ..... processing annotations GTF
Jun 08 07:17:27 ..... inserting junctions into the genome indices
Jun 08 07:18:46 ..... started mapping
Jun 08 08:07:15 ..... finished mapping
Jun 08 08:07:20 ..... started sorting BAM
Jun 08 08:11:48 ..... finished successfully