Updating to new version error

mothur bugs
1

Hey,

Just updated to the newest version (1.24.0) on OSX 10.6.8, running fine prior on 1.23.0, and I now get an error

bash-3.2$ mothur
dyld: Library no loaded: /usr/lib/libedit.3.dylib
Referenced from: /Users/dominiqueponcelet/mothur/mothur
Reason: image not found
Trace/BPT trap
bash-3.2$


Ideas? Mothur is installed to /Users/dominiqueponcelet/mothur/ .
2

Looks like I found my own solution…10.6 uses libedit.2.dylib

Issuing
cd /usr/lib
sudo ln -s libedit.2.dylib libedit.3.dylib


appears to have fixed the issue.
3

Hello mothur friends,

After updating to v1.24 for macOSX-10.6 64bits I gave the following error:

Last login: Wed Mar 14 22:38:55 on ttys000
MacBook-Pro-de-Marc-Lliros-Dupre:~ mlliros$ /Users/mlliros/Downloads/mothur/mothur ; exit;
dyld: Library not loaded: /usr/lib/libedit.3.dylib
Referenced from: /Users/mlliros/Downloads/mothur/mothur
Reason: image not found
Trace/BPT trap
logout

Any idea to solve it?

Thanks friends!

Marc Lliros

4

I just uploaded a new executable to the wiki which should resolve the issue. Thanks for bringing it to our attention!

5

Hi mothur staff

thanks a lot … seems to work fine for me

Cheers

Marc

6

Dear all,

After down-loading the executable you have uploaded it cames out that crashed while “running” rarefaction.single()
I run …

Mac version

Using ReadLine

Running 64Bit Version

mothur v.1.24.0
Last updated: 3/15/2012

mothur > summary.seqs(fasta=/Users/mlliros/fras.fas)

Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 790 790 0 4 1
2.5%-tile: 1 798 798 0 4 2
25%-tile: 1 802 802 0 5 16
Median: 1 806 806 0 5 31
75%-tile: 1 811 811 0 5 46
97.5%-tile: 1 831 831 5 6 59
Maximum: 1 832 832 6 7 60
Mean: 1 808.767 808.767 0.283333 4.86667

of Seqs: 60

Output File Name:
/Users/mlliros/fras.fas.summary


mothur > align.seqs(candidate=/Users/mlliros/fras.fas,template=/Users/mlliros/silva.archaea.fasta,flip=T)

Reading in the /Users/mlliros/silva.archaea.fasta template sequences… DONE.
It took 4 to read 2297 sequences.
Aligning sequences from /Users/mlliros/fras.fas …
60
It took 1 secs to align 60 sequences.


Output File Names: /Users/mlliros/fras.align /Users/mlliros/fras.align.report
mothur > dist.seqs(fasta=/Users/mlliros/fras.align,output=lt) 0 0 59 1

Output File Name:
/Users/mlliros/fras.phylip.dist

It took 1 to calculate the distances for 60 sequences.

mothur > cluster(phylip=/Users/mlliros/fras.phylip.dist,cutoff=0.03)
********************###########
Reading matrix: |||||||||||||||||||||||||||||||||||||||||||||||||||

changed cutoff to 0.03487

Output File Names:
/Users/mlliros/fras.phylip.an.sabund
/Users/mlliros/fras.phylip.an.rabund
/Users/mlliros/fras.phylip.an.list

It took 0 seconds to cluster

mothur > bin.seqs(fasta=/Users/mlliros/fras.fas)
Using /Users/mlliros/fras.phylip.an.list as input file for the list parameter.
unique
0.01
0.02
0.03

Output File Names:
/Users/mlliros/fras.phylip.an.unique.fasta
/Users/mlliros/fras.phylip.an.0.01.fasta
/Users/mlliros/fras.phylip.an.0.02.fasta
/Users/mlliros/fras.phylip.an.0.03.fasta


mothur > get.oturep(phylip=/Users/mlliros/fras.phylip.dist,fasta=/Users/mlliros/fras.fas,list=/Users/mlliros/fras.phylip.an.list) ********************#****#****#****#****#****#****#****#****#****#****# Reading matrix: ||||||||||||||||||||||||||||||||||||||||||||||||||| *********************************************************************** unique 55 0.01 40 0.02 38 0.03 31

Output File Names:
/Users/mlliros/fras.phylip.an.unique.rep.names
/Users/mlliros/fras.phylip.an.0.01.rep.names
/Users/mlliros/fras.phylip.an.0.02.rep.names
/Users/mlliros/fras.phylip.an.0.03.rep.names
/Users/mlliros/fras.phylip.an.0.01.rep.fasta
/Users/mlliros/fras.phylip.an.0.02.rep.fasta
/Users/mlliros/fras.phylip.an.0.03.rep.fasta
/Users/mlliros/fras.phylip.an.unique.rep.fasta


mothur > rarefaction.single() Using /Users/mlliros/fras.phylip.an.list as input file for the list parameter.
or the same ending with mothur > rarefaction.single(list=/Users/mlliros/fras.phylip.an.list)

Both options crashed.

Sorry for that and if someone else found and report the same bug in v.1.24

Again,

Thanks a lot for your work

Marc

7

Hi Marc,
I uploaded version 1.24.1 to the wiki. Thanks for helping us keep mothur as bug free as possible.
-Sarah

8

Thanks Sarah,

I’m going to try it …

Cheers

Marc