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?