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zy-optimistic / GAEP

A genome assembly assessment pipeline.
GNU General Public License v3.0
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Dependencies Error #6

Closed WangZhSi closed 1 year ago

WangZhSi commented 1 year ago

Hi there,

Thank you for the GAEP, our analysis work has been greatly facilitated.

But I met some problems when using it. It seems that GAEP cannot read config correctly, for example, I declare the path of hisat2 in config, and source the env of hisat2, the stderr still cant running NGS mapping. My code as follow:

source env.sh && GAEP pipe -c conf # followed by data dir

the error shows like:

[run_hisat2] Error! Hisat2_build is not found.
[run_hisat2] Check your config file or set it in your environment.
Unknown option: s

In env.sh, I export hisat2 path into $PATH. In config, I declare the path to hisat2 executable file. Could you please find why this happened? Otherwise I can only write the absoltue path into your perl script.

By the way, what is bbtools? I got many searching results, I didn't use it before.

Thanks!

zy-optimistic commented 1 year ago

Thanks for using GAEP.

I have corrected some errors in the code, but I don't think that's where the problem lies. The log shows that 'hisat2_build' is not found, so please check if the 'hisat2_build' executable file is also declared in the config file or exported into the $PATH. If the problem still persists, please let me know, and I will continue to assist you in resolving it.

BBtools is a dependency of BUSCO and can be downloaded from https://jgi.doe.gov/data-and-tools/software-tools/bbtools/. For more information, you can refer to the BUSCO guide available at https://busco.ezlab.org/busco_userguide.html#manual-installation.