Fasta_mothur.eft

cbharder · October 2, 2017, 7:20am

I have trouble using the fasta_mothur.eft format converter when I try to work with the readme for silva 128 (http://blog.mothur.org/2017/03/22/SILVA-v128-reference-files/). I have created it with a content and format just like this:

SUFFIX fasta
BEGIN

(acc).(name)\t*(align_ident_slv)\t*(tax_slv);
*(|export_sequence)

and stored it in my arb/lib/exports folder, but when I open up ARB, the fasta_mothur.eft file just not among the format outputs I can choose from.

I dontr know if the problem is with the installation. I run arb on a Mac 10.10 Yosemite, and I installed it via MacPorts. Dr. Schloss´ quoted page above tells me to store the fasta_mothur.eft in the “/opt/local/share/arb/lib/export/” folder, however, when I install arb I get this filepath:

/Users/[my_username]/arb/arbsrc_15220/lib/export/

When I call the programme in a unix window, I receive these notices:

Ignoring set ARBHOME ‘/opt/local/share/arb’ (overridden by explicit call of ‘/opt/local/bin/arb’)
Using ARBHOME=‘/opt/local/share/arb’
Using properties from /Users/[my_username]/.arb_prop
Please wait while the program ARB is starting …
Waiting for ‘/Users/chribhar/.arb_tmp/sockets/arb_launcher.13651’…
[arb_launcher[0]: Starting ‘arb_ntree SSURef_NR99_128_SILVA_07_09_16_opt.arb’…]
Using properties from ‘/opt/local/share/arb/lib/arb_default/ntree.arb’
Using properties from ‘/opt/local/share/arb/lib/arb_default/status.arb’
ARB: Loading ‘ntree.arb’
ARB: Loading ‘/opt/local/share/arb/lib/arb_default/ntree.arb’ done

ARB: ARB: Loading ‘SSURef_NR99_128_SILVA_07_09_16_opt.arb’
ARB: ARB: no FastLoad File ‘SSURef_NR99_128_SILVA_07_09_16_opt.ARM’ found => loading entire DB
ARB: ARB: Loading ‘SSURef_NR99_128_SILVA_07_09_16_opt.arb’ done

Any advise would be greatly appreciated. Best, Christoffer

pschloss · October 2, 2017, 12:04pm

Can you find the fasta.eft file in your file directory? Is the fasta_mothur.eft file in that directory?

If you do

ls $ARBHOME

at a prompt what do you get?

Pat

cbharder · October 2, 2017, 9:02pm

I can find both the fasta_mothur.eft and the fasta.eft in the arb/arbsrc_15220/lib/export folder where I installed the fasta_mothur.eft, it just simply does not appear to be the same folder in which ARB is looking.

prompting ls $ARBHOME in the arb export folder gives me this:

bio91157:export chribhar$ ls $ARBHOME
GDEHELP SH demo.arb
PERL_SCRIPTS bin lib

pschloss · October 5, 2017, 11:20am

If you do

ls -lth arb/arbsrc_15220/lib/export

what do you get?

MarwaTawfik · September 11, 2021, 5:20pm

Where should I put this command? I am using the arb in conda environment and it worked well till this step. When I tried to export from arb I couldn’t find extension fasta_mothur.eft? how I can create that using the mentioned command in README for the SILVA v138.1 reference files

SUFFIX          fasta
BEGIN
>*(acc).*(name)\t*(align_ident_slv)\t*(tax_slv);
*(|export_sequence)

MarwaTawfik · September 11, 2021, 6:29pm

I also can’t find the directory /usr/lib/arb/lib/export
I exported in my current directory, should I export it the aforementioned directory?
when I used cd /usr/lib/arb/lib/export I couldn’t find
bash: cd: /usr/lib/arb/ no such file or directory
I installed that just in the conda env so I am not a system user, in addition, I can’t install using sudo as I am not a system user

pschloss · September 13, 2021, 1:35pm

Hi Marwa -

Sorry, I don’t use conda. You need to create that file and save it to $ARBHOME/lib/export/. If you type ls $ARBHOME at your prompt what do you get?

Do you really need to go through arb? All of the 16S files are posted to the mothur wiki, so you shouldn’t need to do this unless you’re trying to do something a bit different.

Pat

MarwaTawfik · September 14, 2021, 1:57pm

Many Thanks, Pat for your reply.

Do you mean I can use SILVA v138.1 available on the mothur website without making any changes? the problem is that I can’t find FASTA file in SILVA v138.1 and also I am using V3-V4 region.

So what I can use instead of conda for achieving this? the readme file attached with SILVA v138.1 is asking us to perform those steps: README for the SILVA v138.1 reference files. I wonder there is no ready files (fasta, etc) to be directly used as inputs in workflow steps?

Cheers
Marwa

pschloss · September 14, 2021, 5:21pm

You can find the processed files at Silva reference files.

For the V3-V4 you need to follow the instructions at Customize your reference alignment for your favorite region

mariosoto · January 24, 2022, 8:20pm

Hello Marwa,

Here you can find something could help you with this topic. If you’re using conda, you should change /usr/lib… for your path to arb’s lib folder.

github.com

NorwegianVeterinaryInstitute/BioinfTraining/blob/master/Building_classification_databases.md

# Building rRNA classification databases

In order to understand the taxonomic composition of metagenomic samples it is need to classify sequences against a reference database. However, obtaining and using a database for taxonomic classification isn't trivial and the difficulties can be due to a range of issues you could encounter.
These issues could be due to the sequences you want to classify (is it shotgun data, or is it a marker gene like 16S rRNA, rpoB or another gene), the sequence repository you are using, the taxonomic content of the database, or your classification tool wants to have sequence data in a special format. That means that it is important to obtain a database that is suitable for your data, that has good taxonomic coverage of the taxa you are interested in, and that it is well curated (e.g. contains few misclassifications).

For instance the large NCBI NT or NR database contain sequences from most studied taxa, and when used for shotgun sequence it is able to classify the largest amount of sequences compared to most other databases. However, the taxonomic classification of many sequences using these two database can be problematic due to contamination, misclassifications or simply because people have been sloppy when adding their data to this repositories. Because of that, many initiatives were started to generate curated databases that had a specific audience in mind.

For instance ribosomal RNA sequences are highly abundant in the NCBI NT database, but their classification in that database is problematic and the quality of many sequences is poor. Several initiatives exist that have dealt with these issues and that resulted in different rRNA databases such as [Greengenes](http://greengenes.secondgenome.com/), [Ribosomal database Project](http://rdp.cme.msu.edu/), and the [SILVA database](https://www.arb-silva.de/). Each of these databases come with their own curation method applied to the rRNA data (imported from NCBI NT database), which results in slightly different databases.

My own preference for 16S rRNA database is to use the SILVA database (lucky for me it is considered to be the better database by several people in the field (what ever that means...)).

## Acknowledgements
In this tutorial we will follow the tutorial created by `Pat Schloss` on how to obtain the latest complete SILVA database (version 132) and make it suitable for use with the mothur pipeline. His tutorial is found here: [Building SILVA reference files](http://blog.mothur.org/2018/01/10/SILVA-v132-reference-files/).

## The SILVA database

Before we do anything, take your webbrowser and surf to the [SILVA database](https://www.arb-silva.de/) homepage. We first will explore this resources before starting with the good stuff. You will see something like the image below:
![SILVA homepage](database_tutorial_files/SILVA_homepage.png)

If you are interested in obtaining sequences you can use several options on the SILVA portal. Those are: `Browser`, `Search`, `Aligner` and `Download`. Note that the SILVA database contains sequence data for the small sub unit (SSU) and the large sub unit (LSU) of the ribosome found in prokaryotes and eukaryotes. Those are the 16S / 18S rRNA (SSU) or the 23S / 25S (LSU) rRNA molecules. The SSU database is the larger of the two and contains most sequences, but in principle both can be used. Remember that it is only due to history that most microbiome studies use the 16S rRNA, but that the marker is not the most optimal for classification.

This file has been truncated. show original

It worked for me, should it could help you.

Best regards,

Mario.

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Fasta_mothur.eft

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