Pause SpeciesPrimer

[Lorenzomicro]

Good evening everyone,
I really appreciate your software and the idea behind of it. Letting people, with few skills in IT, design qPCR primer in a fully automated way. I am new to this and I am trying all of my best. I got docker, the species image and the ref_prok_DB.
I start my first query for Enterobacter kobei (113 genomes downloaded) and after 38h my computer is stuck at the prank step, is it OK?
I have a VM on Windows, so I am sure this is increasing the time needed, but I am wondering if there a way to, more or less, predict how much time is left?

Also also on the web browser the user could start or stop the run. There is a way just to pause it??

Thanks
Lorenzo

[biologger]

Hi,
Thanks for your message. 38 h seems a really long time just to get to prank. Prank is usually not a step that takes very long. Of course a VM will slow things down a bit, however if you have several cores and 8-16 GB ram allocated it should run way faster. What are your specifications?

For now I would check if a restart works and the run continues with the prank step. Below 2000 core gene sequences with a reasonable size (100s of bps) this should not need more than an hour.

Unfortunately it is not really possible to predict the run time accurately. It really depends on the number of genomes, core genes and primers and for blast searches also on the database size. Usually the annotation of many genomes and later the primer blast and the primer quality control take most time.

For the pause option, right now it is not implemented in the gui (webpage), however using the commandline option allows to pause the pipeline by sending a stop signal (instead of killing the process) by pressing Ctrl + Z in the terminal, type fg to continue and get the output in the terminal.

Best,
Matt

[Lorenzomicro]

Thanks Matt