Open MohamedAbdalfatah opened 8 months ago
Hi Mo,
Sorry to hear that you are encountering issues! I am not 100% sure where this one comes from to be honest, however I have seen some odd interactions of R dependencies within slurm cluster runs. Anyway the precise error seems to relate to some unexpected shape of the data when trying to combine count output from several of the chunks, you could modify your RAM limit to force zUMIs to chunk up the data in a different way and see how that goes! eg. mem_limit: 50
Thank You, it is working mem_limit: 50 Best
Just curious, what was the fastq.gz file size?
Describe the bug Hi, I'm running ZUMIs for smart-seq data, this is not first time to work with it, I had two projects before and I'm using same scripts I got an erorr it seems to be an R erorr after mappign and quantfication and I don't know how to debug or solve it
This is the log.error file
This is the log output file
To Reproduce
This is Ymal File
project: SCMARATOCOV_01 sequence_files: file1: name: /fastq_dir/combined_fastqs/reads_for_zUMIs.R1.fastq.gz base_definition: cDNA(1-100) file2: name: fastq_dir/combined_fastqs/reads_for_zUMIs.R2.fastq.gz base_definition: cDNA(1-100) file3: name: fastq_dir/combined_fastqs/reads_for_zUMIs.index.fastq.gz base_definition: BC(1-8) reference: STAR_index: references/human_star_ref GTF_file: references/Homo_sapiens.GRCh38.109.gtf additional_STAR_params: '' additional_files: ~ out_dir: /outs num_threads: 20 mem_limit: 0 filter_cutoffs: BC_filter: num_bases: 1 phred: 20 UMI_filter: num_bases: 1 phred: 20 barcodes: barcode_num: ~ barcode_file: fastq_dir/combined_fastqs/reads_for_zUMIs.expected_barcodes.txt automatic: no BarcodeBinning: 0 nReadsperCell: 100 counting_opts: introns: yes downsampling: '0' strand: 0 Ham_Dist: 0 velocyto: no primaryHit: yes twoPass: yes make_stats: yes which_Stage: Filtering Rscript_exec: Rscript STAR_exec: STAR pigz_exec: pigz samtools_exec: samtools
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Please can you help me with this? Best Mo