phyluce_assembly_assemblo_spades memory issues with tmp directory location

[NmHamilton]

Hello,

I am having issues with the amount of temporary files created by the phyluce_assembly_assemblo_spades step - this step creates more temporary files than are allowed by our university's cluster. The spades assembler itself has an option to change the location of tmp_dir, but it appears that phyluce_assembly_assemblo_spades does not - I was wondering if there is a way to change the location in the phyluce pipeline?

[brantfaircloth]

Hi Natalie,

Check out this response to a similar older issue and let me know if you have any other problems.

https://github.com/faircloth-lab/phyluce/issues/62#issuecomment-288411042

[brantfaircloth]

You can also try to edit the spades code in phyluce. specifically, you could edit:

phyluce_assembly_assemblo_spades#L122-L124

So that it adds the last two lines to look like:

       "-o",
       sample_dir,
    “--tmp-dir”,
    “/var/scratch"
   ]

And then add a PATH to some scratch space that works for you.

-b

[NmHamilton]

Hi Brant,

Thank you! Editing the spades code in phyluce was the solution I was looking for, but was unsure the best way to go about it. This was a huge help!

Natalie

[brantfaircloth]

Cool - holler if you have any other issues.