Closed bioramg closed 3 years ago
Hi,
Can you send me the log file? I think the problem is with your config file, some other people had also some similar problems. The config file can get corrupted, but I don't know how (maybe caused by the text editor Are you using Windows, Mac or Linux?
And that problem is always resolved by redownloading the config file...
Thank you for your response. I restarted my server computer and it's working fine with the above-mentioned commands. I would like to know how to set the output path and which one is the output file. I obtained so many output files and could not see which one is the final result?
The output files will always get the tag from the project name in the config fiel, soyou need to change this project name for every run! I will make an output directory option for the next update
Thank you
Hi, I am trying to assemble the plant mitochondrial genome using Novoplasty. I am having issues with memory. My server is having 320 GB RAM, 12 core, and 12 TB hard drive space.
Configuration file: Project:
Project name = plant_mt Type = mito_plant Genome Range = 700000-850000 K-mer = 33 Max memory = 290 Extended log = 0 Save assembled reads = no Seed Input = /home/Novoplasty/295K_contig.fasta Extend seed directly = no Variance detection = Chloroplast sequence = /home/Novoplasty/plant_cp.fasta
Dataset 1:
Read Length = 151 Insert size = 550 Platform = illumina Single/Paired = PE Combined reads = Forward reads = /home/1_paired.fq Reverse reads = /home/2_paired.fq
Heteroplasmy:
MAF = HP exclude list = PCR-free =
Optional:
Insert size auto = yes Use Quality Scores = no
I tried with even 0.1% of raw reads, getting the same error. What could be the problem and how to solve it? Thank you.