mothur

Fasta_mothur.eft

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

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

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

If you do

ls -lth arb/arbsrc_15220/lib/export

what do you get?

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)

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

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

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

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