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ChiLiubio / microeco_tutorial

Documentation for microeco package
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Tax4Fun2 Error #4

Open bioengineer opened 2 years ago

bioengineer commented 2 years ago

I get the following error message with Tax4Fun2: "Error in t1$cal_tax4fun2(blast_tool_path = "ncbi-blast-2.5.0+/bin", path_to_reference_data = "Tax4Fun2_ReferenceData_v2", : Tax4Fun2 ReferenceData folder--test_prediction is not existed!"

Initially I had this error on my own data so I attempted to run the microeco-tutorial.Rmd and got the same error.

ChiLiubio commented 2 years ago

Hi. The command seems like not integrated. Could you paste your whole running steps? I guess you do not have a directory named test_prediction, which will be used to store all the intermediate files. If TRUE, please create one manually or use command dir.create("test_prediction")

Best, Chi

bioengineer commented 2 years ago

I downloaded the microeco_tutorial-0.11.0 file and moved it to my home folder. I ran the following in the microeco-tutorial.Rmd file.

data(dataset) t1 <- trans_func$new(dataset)

create a directory for result and log files

dir.create("test_prediction")

https://chiliubio.github.io/microeco_tutorial/intro.html#tax4fun2 for installation

ignore blast_tool_path parameter if blast tools have been in path

the function can search whether blast tool directory is in the path, if not, automatically use provided blast_tool_path parameter

t1$cal_tax4fun2(blast_tool_path = "ncbi-blast-2.5.0+/bin", path_to_reference_data = "Tax4Fun2_ReferenceData_v2",

  • database_mode = "Ref99NR", path_to_temp_folder = "test_prediction") Error in t1$cal_tax4fun2(blast_tool_path = "ncbi-blast-2.5.0+/bin", path_to_reference_data = "Tax4Fun2_ReferenceData_v2", : Tax4Fun2 ReferenceData folder--test_prediction is not existed!

I verified that the folder "test_prediction" is being created and it is located in the same folder as the "microeco-tutorial.Rmd" file.

Owl0928 commented 1 year ago

Hello Chi, I had the same problem, has the problem been solved？

ChiLiubio commented 1 year ago

Hi. Do you have a reference data folder named "Tax4Fun2_ReferenceData_v2"? It is necessary for the program to find the near species related to the ASV/OTU. Please download it as the tutorial shows (https://chiliubio.github.io/microeco_tutorial/intro.html#tax4fun2). 图片

Owl0928 commented 1 year ago

Sorry, I ignored this, now it worked, thanks Chi for you excellent job for freshman like me.