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Error in alldt[[i]][[2]] : subscript out of bounds #377
Comments
Hi Mo, Sorry to hear that you are encountering issues! |
Thank You, it is working mem_limit: 50 |
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
Screenshots
If applicable, add screenshots to help explain your problem.
Desktop (please complete the following information):
Please can you help me with this?
Best
Mo
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