Step 3. 'Combining and annotating blast files'

[plhm]

Hello there, jtlovell. Thank you so much for GENESPACE. This is really a handy piece of software. I'm messaging you because GENESPACE has been stuck at Step 3 for almost 10 hours. It quickly went through steps 1 and 2, but has since gotten stuck at Step3, after the following message: | Generating dotplots for all hits ... I am performing the analysis across 5 diploid vertebrates with a haploid genome size between 1.5 and 2Gb. Is this a common waiting time for this step? Is there any way I can multithread GENESPACE to speed up this process? Best, P

[jtlovell]

I think its likely related to plotting ... do you have a lot of scaffolds or something? You can try re-running with init_windows(..., dotplots = "never")

[plhm]

Hi, John.

Thanks for the message. I appreciate it.

Here are the functions I ran:

`print("Initialize genespace.") gpar <- init_genespace( wd = wd, path2mcscanx = path2mcscanx)

print("Run genespace.") out <- run_genespace(gpar, overwrite = T)`

Could I do init_genespace(...,dotplots="never") instead?

P

On Tue, Mar 26, 2024 at 11:33 AM John Lovell @.***> wrote:

I think its likely related to plotting ... do you have a lot of scaffolds or something? You can try re-running with init_windows(..., dotplots = "never")

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[jtlovell]

yes - see ?init_genespace there are lots of parameters that can be modified, including dotplots