Error with usearch

Microbial community profiling ShortBRED
1

Hello,
I installed ShortBRED using conda (pyhton2.7) and usearch v11.
After running sample files, i got the following error

Checking dependencies…
Traceback (most recent call last):
File “/home/scebmeta/bin/miniconda3/envs/shortbred/bin/shortbred_identify.py”, line 156, in
src.CheckDependency(args.strUSEARCH,"",“usearch”)
File “/home/scebmeta/bin/miniconda3/envs/shortbred/bin/src/init.py”, line 36, in CheckDependency
raise IOError("\nShortBRED was unable to find " + strIntendedProgram + " at the path " + strCmd + "\nPlease check that the program is installed and the path is correct. Please note that ShortBRED will not be able to use the unix alias for the program.")
IOError:
ShortBRED was unable to find usearch at the path usearch

usearch is in path.
I renamed from usearch11.0.667_i86linux32 to usearch and moved to /home/scebmeta/bin/miniconda3/envs/shortbred/bin/.
I don’t have src folder.
Do i need to move my usearch somewhere else or do i need to install another version of usearch or something is wrong?
shortbred_identify.py --help is working.
Thanks,
Khem

2

For this to work you want to be able to call usearch from any working directory and see the program’s help menu. That’s the typical meaning of usearch being “in the PATH.” If the issue is that you have a usearch binary with a different name, you can do something like create a link to that binary with the name usearch in a location that is in the path.

3

hello, have you solve?