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dhcai21 / RVHaplo

A viral haplotype reconstruction tool for long reads.
GNU General Public License v3.0
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Over 8 Hour Processing Time for `mcp_read_graph` #7

Open jonathan-bravo opened 1 year ago

jonathan-bravo commented 1 year ago

Hey Dehan,

I was processing some of my samples and they are taking much longer than what was mentioned in the paper for run time (w/ 8 CPU ~100 min). 3 of the samples I was testing did not finish creating the mcp_read_graph and they had been running for over 8 hours with 32 CPU cores. I also made sure that if the samples had > 50k reads that the -sg n flag was used.

I was wondering if you might be able to help me figure out why it could be taking so long.

Cheers, Johnny

dhcai21 commented 1 year ago

Hi Johnny,

Could you please share the log information and, if possible, provide the data for further investigation?

Thanks, Dehan

jonathan-bravo commented 1 year ago

Hey Dehan,

I am not quite sure which log information you are requesting. There was no error, the program just took a very long time. I will make a new google drive link and upload the files and send the link via email.

Cheers, Johnny

jonathan-bravo commented 1 year ago

I just sent an email containing the link to the data and the shell file I am using to run RVHaplo.