Question

Tax4Fun2 - error

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2.8 years ago

ymj ▴ 10

Hi, I want to use Tax4Fun2 for annotating metabolic potential to microbial communities. I installed everything successfully. I have tested reference data, built the dependencies, and added the bin to PATH. (according to : https://github.com/bwemheu/Tax4Fun2)

When trying to run with the test data using the command: runRefBlast(path_to_otus = "~/Thesis_Data/seqs/seqs.fasta", path_to_reference_data = PATH, path_to_temp_folder = "~/Thesis_Data/seqs/REF99NR", database_mode = "Ref99NR", use_force = T, num_threads = 4) Then, I get this: Copy and generate database Reference blast started Error in if (file.size(path_to_blast_file) == 0) stop("Blast file empty!") : missing value where TRUE/FALSE needed

Anyone has encountered the same problem and knows a solution?

I used tax4fun version 1.1.5.

Thank you in advance!

tax4fun silva blast • 4.3k views

ADD COMMENT • link updated 7 months ago by drstalinantony28 • 0 • written 2.8 years ago by ymj ▴ 10

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I had have the same problem.

ADD REPLY • link 2.7 years ago by fabricio.motteran • 0

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I have the same problem with this package. It is no more maintained on github. Plz if you have a solution for that post here!

Thank you

ADD REPLY • link 2.7 years ago by Claire • 0

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Yes, I solved it a few weeks ago. I remember the error was in the specification of the paths (at least, it was for me). So I did as follows: (change your paths to format : "C:/Users/NAME/folder..."

otus_path <- "path to sequences (fasta)" 
temp_path <- "path to an empty temporal folder"
otu_table_path <- "path to your OTU table"

runRefBlast(path_to_otus = otus_path, 
            path_to_reference_data = PATH, 
            path_to_temp_folder = temp_path, 
            database_mode = "Ref100NR", 
            use_force = FALSE, num_threads = 6)

This worked for me :) let me know if that helped

ADD REPLY • link 2.7 years ago by ymj ▴ 10

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Hi ymj and everybody,

I am trying the above code in R, but always I get the next ERROR:

  PATH = "~/d631a66f-81da-495d-8136-67bc214cb51d2/Tax4Fun2/Tax4Fun2_ReferenceData_v2/"

  runRefBlast(path_to_otus = "~/d631a66f-81da-495d-8136-67bc214cb51d2/Tax4Fun2/R/fasta", 
            path_to_reference_data = PATH, 
            path_to_temp_folder = "~/d631a66f-81da-495d-8136-67bc214cb51d2/Tax4Fun2/R/Ref100NR", 
            database_mode = "Ref100NR", 
            use_force = T, num_threads = 4)

  chmod: can't access to '/home/juanm/d631a66f-81da-495d-8136-67bc214cb51d2/Tax4Fun2/R/Tax4Fun2_ReferenceData_v2//blast_bin/bin/blastn': It doesn't exist the file or directory
sh: 1: /home/juanm/d631a66f-81da-495d-8136-67bc214cb51d2/Tax4Fun2/R/Tax4Fun2_ReferenceData_v2//blast_bin/bin/blastn: not found
**Error in system(command = paste(blast_bin, "-help"), intern = T) : 
  error in running command**
>

But all these folders and files have root permissions.And also I have tried it using nautilus, but the error is the same.

Please, could you help me to solve this error if you know how?.

I use Ubuntu 16.0 and R 4.1.1.

Thank you very much.strong text

ADD REPLY • link updated 2.3 years ago by GenoMax 147k • written 2.3 years ago by j6163mls • 0

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Sorry,

The PATH that I wrote before (my last post) is not correct.The PATH correct is :

PATH = "~/d631a66f-81da-495d-8136-67bc214cb51d2/Tax4Fun2/R/Tax4Fun2_ReferenceData_v2/"

Thank you

ADD REPLY • link 2.3 years ago by j6163mls • 0

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can't access to '/home/juanm/d631a66f-81da-495d-8136-67bc214cb51d2/Tax4Fun2/R/Tax4Fun2_ReferenceData_v2//blast_bin/bin/blastn'

Error is about not being able to find blastn executable. Where is your blast install located? Make sure that directory is in your $PATH or Tax4Fun2 is configured correctly to find blastn.

ADD REPLY • link 2.3 years ago by GenoMax 147k

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Thank you Genomax for your answer,

My blast install is located into the folder Tax4Fun2_ReferenceData_v2 (it includes the bin folder with blastn inside).

Now I had export PATH (as you told me) :

(base) juanm@juanm-Compaq-CQ58-Notebook-PC:~$ export PATH=$PATH:/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d2/Tax4Fun2/R/Tax4Fun2_ReferenceData_v2/bin/blastn

And when I try again in R the runRefBlast() script, the output is the same (the same ERROR).

Please, could you write me the code of $export PATH and the runRefBlast() script to solve this ERROR?

Thank you very much for your help.

ADD REPLY • link 2.3 years ago by j6163mls • 0

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You need to set the PATH to include the directory containing the blastn executable. So use the following and see if that fixes the issue:

export PATH=$PATH:/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d2/Tax4Fun2/R/Tax4Fun2_ReferenceData_v2/bin/

ADD REPLY • link 2.3 years ago by GenoMax 147k

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Again the same ERROR:

  (base) juanm@juanm-Compaq-CQ58-Notebook-PC:~$ export PATH=$PATH:/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d2/Tax4Fun2/R/Tax4Fun2_ReferenceData_v2/bin/

   (base) juanm@juanm-Compaq-CQ58-Notebook-PC:~$ R

R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-conda-linux-gnu (64-bit)

> library(Tax4Fun2)
> library(phyloseq)
> runRefBlast(path_to_otus = "media/juanm/d631a66f-81da-495d-8136-67bc214cb51d2/Tax4Fun2/R/fasta", 
            path_to_reference_data = PATH, 
            path_to_temp_folder = "media/juanm/d631a66f-81da-495d-8136-67bc214cb51d2/Tax4Fun2/R/Ref100NR", 
            database_mode = "Ref100NR", 
            use_force = T, num_threads = 4)

chmod: can't access to '/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d2/Tax4Fun2/R/Tax4Fun2_ReferenceData_v2//blast_bin/bin/blastn': It doesn't exist the file or directory
sh: 1: /media/juanm/d631a66f-81da-495d-8136-67bc214cb51d2/Tax4Fun2/R/Tax4Fun2_ReferenceData_v2//blast_bin/bin/blastn: not found
Error in system(command = paste(blast_bin, "-help"), intern = T) : 
  error in running command
>

Thank you

ADD REPLY • link updated 2.3 years ago by GenoMax 147k • written 2.3 years ago by j6163mls • 0

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So the program path being checked (and which generates the error that blastn is not found) is

/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d2/Tax4Fun2/R/Tax4Fun2_ReferenceData_v2//blast_bin/bin/blastn

Where as you are setting the $PATH to

/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d2/Tax4Fun2/R/Tax4Fun2_ReferenceData_v2/bin/

those two paths are not the same. Which exact directory is your blastn executable located in?

ADD REPLY • link 2.3 years ago by GenoMax 147k

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    Hi GenoMax,

    My blastn executable is located in the directory (inside of the bin folder):

   " /media/juanm/d631a66f-81da-495d-8136-67bc214cb51d2/Tax4Fun2/R/Tax4Fun2_ReferenceData_v2/bin/blastn"



   Thank you

ADD REPLY • link 2.3 years ago by j6163mls • 0

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If that is correct then you need to make sure that Tax4Fun2 is configured accordingly. Currently it appears to be looking for blastn in /media/juanm/d631a66f-81da-495d-8136-67bc214cb51d2/Tax4Fun2/R/Tax4Fun2_ReferenceData_v2//blast_bin/bin/.

ADD REPLY • link 2.3 years ago by GenoMax 147k

score 0 · Answer 1 · 2024-04-24

You have to follow this step to solve the issue. (Mostly this problem occurs in the Windows version)

If you are using R studio in Windows, try to Install the standalone version of the BLAST (https://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/)
Once you have done the installation, go to the installation directory in Windows, (Example: C:\Program Files\NCBI\blast-2.15.0+\bin)
copy all the binary files from the folder, and paste (replace) them into the binary folder of Tax4Fun2_ReferenceData_v2 (Tax4Fun2_ReferenceData_v2\blast_bin\bin).
That's it. Now you can run the command. It will work.

good luck....

Dr. Antony Stalin