Question: Minia stuck - I don't know if my routine is still running
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gravatar for barbarahufnagel
4 months ago by
barbarahufnagel0 wrote:

Hi, I am trying to run MINIA 2.0.7 on my mac to assembly a genome of estimated size of 570Mb. The data is from a illumina 125 pair-end run.

It goes through the steps:

  • counting of the k-mers (kmer size=21) ,
  • Initialization (100%)
  • built hash values (99.4%)
  • assign values (100%)
  • populate (99.4%).

Then starts function [others] - there are more than 100 lines with this function. I started to run it 72hs ago. Last time the file .h5 (that has been created) was updated were 5h after the beginning of the process...

Is it gonna have an end or it is stucked and will crash at some point?

(It is the third time I am running it and the other times it crashed at this stage. This time I am running it on a more powerful machine and I has hoping it would work...)

minia • 211 views
ADD COMMENTlink written 4 months ago by barbarahufnagel0

This time I am running it on a more powerful machine

Does this machine have more RAM than the last two? If your program has run of memory there is not much happening beyond this point. Use "Activity monitor" on your Mac to check memory consumption (and while you are there take a look at CPU usage).

ADD REPLYlink modified 4 months ago • written 4 months ago by genomax39k

Hi @genomax , Yes. This computer has more Ram memory (16gb vs 8gb of before) . I'm keeping on track the run with the "Activity monitor" all the time, however it doesn't seem to be consuming too much memory. For the CPU usage it has some picks close to 100% sometimes, but it fast drops again. Do you think this is still active?

ADD REPLYlink written 4 months ago by barbarahufnagel0

72h seems like an awful long time to have nothing happen but if you are sure that there is free memory available and the actual minia (or which ever program minia is running at the moment) is still working then you should wait. I have "tagged" Rayan who may be able to provide more information but be aware that Rayan has not logged into Biostars for 5 weeks.

ADD REPLYlink modified 4 months ago • written 4 months ago by genomax39k

Ok! Thanks genomax! I will wait for it...

ADD REPLYlink written 4 months ago by barbarahufnagel0

Tagging: Rayan Chikhi

ADD REPLYlink written 4 months ago by genomax39k

Apologies, I do not get Biostar notifications through my email for some reasons. How much disk space and memory do you have on this machine? Did you end up getting an assembly with version 2.0.7? If not, I could advise trying the very latest version from the Github, following the compilation instructions there (https://github.com/GATB/minia)

ADD REPLYlink modified 3 months ago • written 3 months ago by Rayan Chikhi1.2k
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