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liuql2019 / VFM

VFM: Mining phages from metagenomes based on gene and genome composition
GNU General Public License v3.0
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Checkpoint #1

Open Handymanalan opened 4 years ago

Handymanalan commented 4 years ago

Hi QiaoLiang,

Thanks for the program. Can VFM run from certain checkpoints? VFM stopped as it reaches the maximum time limit I can have on the HPC. I am wondering if VFM can run based on the hmm/prokka/blastp files already produced.

Cheers

Alan

liuql2019 commented 4 years ago

Hi Alan,

Thanks for your interest. It maybe takes long time to run VFM because of gene prediction, pVOG scan and COG scan. In fact, if some of the three steps are finished, you can restart VFM from the checkpoints behind them by commenting out the corresponding lines of the code for the finished steps. For example, if the hmm/prokka/blastp files already produced, you can comment out line 638, line 645 and line 649 in the file of methods.py. And restart VFM again to bypass these steps.

Thank you. Liu