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diriano / ploidyNGS

Explore ploidy levels from NGS data alone
GNU General Public License v3.0
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How long it takes ploidyNGS to finish a job? #1

Closed danshu closed 7 years ago

danshu commented 7 years ago

Hi,

I have been running ploidyNGS for a whole day and I want to know how long it takes ploidyNGS to finish a job? And can it be multi-threaded? ploidyNGS is just keep runnning and doesn't produce any putputs or messages.

Best, Quan

danshu commented 7 years ago

After running for a whole day, I finally have output files. However. then there is an error in the Rscript part then "Execution halted". ploidyNGS is keeping running consuming a lot of memory and the previous outputfile was gone.

Basically It seems that ploidyNGS only uses a single thread while reads a lot into the memory, which is not that efficient. After producing the outputfile, Rscript reads that file trying to do plotting, but I don't understand why the outputfile was deleted. In my case an eror during the plotting part may waste a whole day's work. If the outputfile wasn't removed, then I can simply rerun the Rscript.

These are two my concerns after trying ploidyNGS. It is definitely a useful tool but it can be more user-friendly.

Best, Quan

SantosRAC commented 7 years ago

Hello Quan,

Thanks for trying ploidyNGS, especially for your comments about the software.

I have updated the ploidyNGS script. It is no longer deleting the intermediary file (.tbl), so you could try to run the RScript.

I will be traveling for the next few months, so unfortunately I probably won't have time to implement the multithreading. But I agree that it is important and I will try to work on it as soon as possible.

All the best,

Renato Santos.

On Sat, Nov 12, 2016 at 2:34 AM, danshu notifications@github.com wrote:

After funning for a whole day, I finally have output files. However. then there is a error in the Rscript part then "Execution halted". ploidyNGS is keeping running consuming a lot of memory and the previous outputfile was gone.

Basically It seems that ploidyNGS only uses a single thread while reads a lot into the memory, which is not that efficient. After producing the outputfile, Rscript reads that file trying to do plotting, but I don't understand why the outputfile was deleted. In my case an eror during the plotting part may waste a whole day's work. If the outputfile wasn't removed, then I can simply rerun the Rscript.

These are two my concerns after trying ploidyNGS. It is definitely a useful tool but it can be more user-friendly.

Best, Quan

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danshu commented 7 years ago

Thanks!