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:
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 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: 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
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
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
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
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?