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zifanzhu / MicroPro

A microbial profiling framework for metagenomic analysis
GNU General Public License v3.0
24 stars 6 forks source link

Does this pipeline require root permission? #1

Closed wangjianshou closed 5 years ago

wangjianshou commented 5 years ago

Does this pipeline require root permission?

zifanzhu commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

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

Zifan