Does this pipeline require root permission?

[wangjianshou]

Does this pipeline require root permission?

[zifanzhu]

Hi wangjianshou,

Sorry for the late reply!

Root permission is platform dependent. Since MicroPro requires a few dependencies, the installation of some of them might need root permission on your machine (or not). I encourage you to try the installation yourself and see how it goes. Let me know if you have any more questions.

Best,
Zifan

[wangjianshou]

Hi zifanzhu,
thank you for your reply firstly.
when running this pipeline, I get this error which generated by 'scripts/u_v_abund.R':

File '4_virfinder/4_4_vf_summary/wc_vf_filtered' does not exist

'scripts/u_v_abund.R' belongs to 'rule unknown_v_abund'.

I confirmed that this file called 'wc_vf_filtered' does not exist, but I cannot find which step can gengrate it, could you give me some help or advice? thank you in advance.
Best,
wanjianshou

[zifanzhu]

Hi wanjianshou,

This is a bug fixed in the latest MicroPro. You may replace your 'snake-binning-P' file with the new one and run the Snakemake command again (without deleting old results). Snakemake will skip what you've obtained and run what you didn't get. Let me know if this solves your problem.

Best,
Zifan

[wangjianshou]

Hi,
thank you very much.
It is already running successfully. But there is a small bug in this script called "scripts/u_v_abund.R":

line 95: vp <- v_ctg / ctg

But both of v_ctg and ctg are instances of data.table class. So I think this line should be vp <- v_ctg[1,1] / ctg[1,1]

Thank you
wangjianshou

[zifanzhu]

Yes, you're right. I fix it now. Thanks a lot!

Zifan