Installation: Tax4Fun2 package are not found and github repository is not maintained anymore
2
2
Entering edit mode
2.5 years ago
Elsa ▴ 20

Hi everyone!

I have tried to find the R package Tax4Fun2 from the paper (https://pubmed.ncbi.nlm.nih.gov/33902725/) . This R package lets analizes the microbiome in an easy way to predict functional profiles from metagenomic 16S rRNA data.

However, I have not found the package in R CRAN packages, neither in the github refered in the original paper (https://github.com/bwemheu/Tax4Fun2) or the Tax4Fun page (http://tax4fun.gobics.de/).

I am looking for Tax4Fun2 because gives higher accuracies than PICRUSt and Tax4Fun.

Any help will be grateful!

Best,

E

Tax4Fun2 • 6.4k views
ADD COMMENT
0
Entering edit mode

Tax4Fun2 because gives higher accuracies than PICRUSt

They tested Tax4Fun2 (2020) against PICRUSTt version 1, which is very old (2013). In this paper on the other hand, Tax4Fun2 actually performs worse than PICRUSt2

ADD REPLY
0
Entering edit mode

Hello , I also have the same problem. Did you find repositories for installing T4F2 and T4F please ? if not what did you use as an alternative and are you satisfied with the results of the alternative tool ? please answer !!

ADD REPLY
0
Entering edit mode

please I am trying to install and use Tax4fun2. but do you have the SILVA_132_SSURef_NR90.fasta file? I attempted to locate it in the Silva Database, but I couldn't find it.

https://www.arb-silva.de/no_cache/download/archive/release_132/ARB_files/

Tax4Fun2 requires the SILVA_132_SSURef_NR90.fasta file specifically... Thank you so much

ADD REPLY
0
Entering edit mode

You just need to look through other directories. This file is the closest to what you want:

https://www.arb-silva.de/fileadmin/silva_databases/release_132/Exports/SILVA_132_SSURef_Nr99_tax_silva.fasta.gz

After unpacking, you can either rename the file to SILVA_132_SSURef_NR90.fasta or change the code to use the file you have.

ADD REPLY
0
Entering edit mode

Thank you so much. I downloaded it and renamed it, now I need to download and install prodigal_v2.6.3

Thank so much

ADD REPLY
0
Entering edit mode

I have downloaded it from here: https://mirrors.opensource.is/ubuntu/pool/universe/p/prodigal/

prodigal_2.6.3.orig.tar.gz

but there is no file named: prodigal.macos

ADD REPLY
0
Entering edit mode
assignFunction(genome_file = "OneProkaryoticGenome.fasta", 
               file_extension = "fasta", 
               path_to_reference_data = "Tax4Fun2_ReferenceData_v2", 
               num_of_threads = 1, fast = TRUE)

chmod: Tax4Fun2_ReferenceData_v2/TOOLS/prodigal_v2.6.3/prodigal.macos: No such file or directory
chmod: Tax4Fun2_ReferenceData_v2/TOOLS/diamond_v0.9.24/diamond.macos: No such file or directory

Error in system(command = paste(path_to_diamond, "help"), intern = T,  : 
  error in running command

what should i do? I have Tax4Fun2_ReferenceData_v2/TOOLS/prodigal_v2.6.3/prodigal.macos (renamed it prodigal), Tax4Fun2_ReferenceData_v2/TOOLS/diamond_v0.9.24/diamond.macos (renamed it: diamond)

ADD REPLY
0
Entering edit mode

Mai Abdelmonem : Stop posting errors and comments as new answers. Submit answer is only for new answers to the original question.

ADD REPLY
0
Entering edit mode

Okay, I see. Sorry for that

ADD REPLY
1
Entering edit mode
2.5 years ago
Mensur Dlakic ★ 28k

I searched GitHub for Tax4Fun2 and found this:

https://github.com/ZihaoShu/Tax4Fun2

ADD COMMENT
0
Entering edit mode

This is a repository for a project that uses tax4fun2, not the repository that documents T4F and provides it for download/installation. All repositories for installing T4F2 and T4F seem to have been removed from the internet in the last few months.

ADD REPLY
0
Entering edit mode

Hello , I also have the same problem. Did you find repositories for installing T4F2 and T4F please ? if not what did you use as an alternative and are you satisfied with the results of the alternative tool ? please answer !!

ADD REPLY
1
Entering edit mode

https://github.com/ZihaoShu/Tax4Fun2 has tar file Tax4Fun2_1.1.5.tar.gz, download and install from source.

install.packages("Tax4Fun2_1.1.5.tar.gz", repos = NULL, type = "source")
ADD REPLY
0
Entering edit mode
8 months ago
Viviane • 0

Hello! I was confused as well.

When installing Tax4Fun2, Follow this: https://github.com/songweizhi/Tax4Fun2_short_tutorial?search=1

ADD COMMENT

Login before adding your answer.

Traffic: 1735 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6