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ruanjue / wtdbg2

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly
GNU General Public License v3.0
513 stars 94 forks source link

Estimation of the operation time #125

Closed jacqgg closed 5 years ago

jacqgg commented 5 years ago

Hi! Is it possible to estimate the duration of the program? I am interested in estimating the time the ctg.lay.gz graph was created. I have a large input data. Thanks!

ruanjue commented 5 years ago

I am not sure. If you find the file size doesn't increase for a long time, there must be some bug.

jacqgg commented 5 years ago

Ok, thank you. This would be a useful option - how to predict how long it will take.

jacqgg commented 5 years ago

Maybe you know how long it will take to produce ctg.lay.gz file from ~60 gigabases input fastq? I have available 500Gb RAM and 88 threads

ruanjue commented 5 years ago

Shold be very fast, at most 30 mins.

jacqgg commented 5 years ago

INFO: almost 60 gigabases input fastq took ~300 mins, but with "-x ont" parameter (88 threads).

ruanjue commented 5 years ago

Did you mean total wall-clock time or time for output .ctg.lay.gz file?

jacqgg commented 5 years ago

Total time from the beginning (reading reads took 9 mins) to end of standard wtdbg2 run. The longest part took 4,5h.

ruanjue commented 5 years ago

Total time is ok.