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ndierckx / NOVOPlasty

NOVOPlasty - The organelle assembler and heteroplasmy caller
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Out of Memory / 'Max memory' can only be an integer, the amount is always in GB of RAM, don't add a unit! #150

Closed bioramg closed 3 years ago

bioramg commented 3 years ago

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.

  1. If I do not mention anything on Max memory option in the configuration file, I am getting a message "Retrieve Seed...Out of Memory!" and could not run any other programs for at least 24 h.
  2. If I mention 290 on Max memory option in the configuration file, then I am getting a message " 'Max memory' can only be an integer, the amount is always in GB of RAM, don't add a unit ! "

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.

ndierckx commented 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...

bioramg commented 3 years ago

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?

ndierckx commented 3 years ago

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

bioramg commented 3 years ago

Thank you