Open lysurgeon opened 3 months ago
Describe the bug I have successfully constructed the STAR-index that contains the genomeParameters.txt file. but error was “genomeParameters.txt: No such file or directory”。How can I deal with this problem?
To Reproduce yaml file project: SS sequence_files: file1: name: /home/ubuntu/raw/A1_1.fastq.gz base_definition: cDNA(1-60) file2: name: /home/ubuntu/raw/A1_2.fastq.gz base_definition: cDNA(1-50) reference: STAR_index: /home/ubuntu/ref/hg38 GTF_file: /home/ubuntu/ref/genes.gtf additional_STAR_params: '' additional_files: ~ out_dir: /home/ubuntu/out num_threads: 32 mem_limit: 0 filter_cutoffs: BC_filter: num_bases: 1 phred: 20 UMI_filter: num_bases: 1 phred: 20 barcodes: barcode_num: null barcode_file: null barcode_sharing: '' automatic: yes BarcodeBinning: 1 nReadsperCell: 100 demultiplex: no counting_opts: introns: yes downsampling: '0' strand: 0 Ham_Dist: 0 write_ham: no velocyto: no primaryHit: yes twoPass: yes make_stats: yes which_Stage: Filtering Rscript_exec: Rscript STAR_exec: STAR pigz_exec: pigz samtools_exec: samtools
Screenshots
Describe the bug I have successfully constructed the STAR-index that contains the genomeParameters.txt file. but error was “genomeParameters.txt: No such file or directory”。How can I deal with this problem?
To Reproduce yaml file project: SS sequence_files: file1: name: /home/ubuntu/raw/A1_1.fastq.gz base_definition: cDNA(1-60) file2: name: /home/ubuntu/raw/A1_2.fastq.gz base_definition: cDNA(1-50) reference: STAR_index: /home/ubuntu/ref/hg38 GTF_file: /home/ubuntu/ref/genes.gtf additional_STAR_params: '' additional_files: ~ out_dir: /home/ubuntu/out num_threads: 32 mem_limit: 0 filter_cutoffs: BC_filter: num_bases: 1 phred: 20 UMI_filter: num_bases: 1 phred: 20 barcodes: barcode_num: null barcode_file: null barcode_sharing: '' automatic: yes BarcodeBinning: 1 nReadsperCell: 100 demultiplex: no counting_opts: introns: yes downsampling: '0' strand: 0 Ham_Dist: 0 write_ham: no velocyto: no primaryHit: yes twoPass: yes make_stats: yes which_Stage: Filtering Rscript_exec: Rscript STAR_exec: STAR pigz_exec: pigz samtools_exec: samtools
Screenshots