sh: 1: arb_phylo: not found

[guest]

When calling Create SAI Using . . > Filter by Base Frequency I get the following error: [Action: 'arb_phylo &'] sh: 1: arb_phylo: not found

I set already and alias for arb_phylo which point to arb/bin/arb_phylo but that did not fix it.

[westram]

Replying to guest:

When calling Create SAI Using . . > Filter by Base Frequency I get the following error: [Action: 'arb_phylo &'] sh: 1: arb_phylo: not found

I set already and alias for arb_phylo which point to arb/bin/arb_phylo but that did not fix it.

There is no need to set up an alias for arb_phylo - if arb does not find it, your installation is broken in some way.

I guess you did not setup your shell environment as described on page 1 of ​ARB_install.pdf. Please try to do as described there.

If that doesn't help please try to reinstall arb.

If that still does not help, please comment on this ticket and provide us with the information requested ​here.

[guest]

After reinstalling ARB, according to the ARB_install.pdf I still get the same error:

[Action: 'arb_phylo &'] sh: 1: arb_phylo: not found

system info:

• arb: arb_5.5
• database: protein database self created
• unix: Ubuntu 12.04 LTS (on Oracle Virtual Box)
• .bashrc:

# ARB path and alias

ARBHOME=/home/tv195/ARB;export ARBHOME

LD_LIBRARY_PATH=${ARBHOME}/lib:${LD_LIBRARY_PATH} export LD_LIBRARY_PATH PATH=${ARBHOME}/bin:${PATH} export PATH

alias arb=/home/tv195/ARB/bin/arb

echo "ARB" # to see if the script has been read

Thank you, Chris

[westram]

Hi Chris,

strange! I have tested that with arb_5.5 (as well 12.04 in VB), works.

1. try whether behavior is the same with $ARBHOME/demo.arb
   • if it works there, your database must be the cause
2. else startup arb. in the main window run Start XTERM from the Tools menu. In the terminal showing up, run the following commands and send me the output

   which arb_phylo
   echo $ARBHOME
   ls -al $ARBHOME/bin/arb_phylo
   file $ARBHOME/bin/arb_phylo
   ldd $ARBHOME/bin/arb_phylo
   

[guest]

Thanks, tried demo.arb - get the same error:

ARB: Loading '/home/tv195/ARB/demo.arb' ARB: no FastLoad? File '/home/tv195/ARB/demo.ARM' found: loading entire database ARB: Loading '/home/tv195/ARB/demo.arb' done

[Action: 'arb_phylo &'] sh: 1: arb_phylo: not found

ran it: which arb_phylo arb_phylo not found

echo $ARBHOME /usr/lib/arb

ls -al $ARBHOME/bin/arb_phylo ls: cannot access /usr/lib/arb/bin/arb_phylo: No such directory

file $ARBHOME/bin/arb_phylo no such file or directory

ldd $ARBHOME/bin/arb_phylo

no such file or directory

[westram]

Replying to guest:

Your $ARBHOME points to the wrong directory - either your ~/.bashrc is not executed (e.g. because you use a different shell) or something is ignored or the settings are overwritten elsewhere.

echo $ARBHOME

/usr/lib/arb

Wanted result would be /home/tv195/ARB.
/usr/lib/arb is chosen as fallback if ARBHOME is undefined.

Even w/o any definitions in ~/.bashrc the following command should work:

export ARBHOME=/home/tv195/ARB; cd $ARBHOME; bin/arb

[guest]

Thank you, using this I get:

export ARBHOME=/home/tv195/ARB; cd $ARBHOME; bin/arb

Using ARBHOME='/home/tv195/ARB' Please wait while the program ARB is starting ….. \[\e]0;\u@\h: \w\a\]${debian_chroot:+($debian_chroot)}\u@\h:\w\$ arb_ntree: error while loading shared libraries: libXm.so.3: cannot open shared object file: No such file or directory ARB done

[guest]

I just discovered that ARB is already pre-installed in this version of bio_linux on ubuntu 12.04 LTS. So my path in the. bashrc to the ARB version I installed was actually ignored and when I typed "arb" then the pre-installed version was started. However the arb_phylo not found error still exists. I found the pre-installed ARB:

/usr/bin/arb [ 9:55PM] Using ARBHOME='/usr/lib/arb' Please wait while the program ARB is starting ….. tv195@tv195-VirtualBox?/ ARB: Loading '.arb_prop/ntree.arb' [ 9:57PM] ARB: Loading '/home/tv195/.arb_prop/ntree.arb' done

but the error still exists:

[Action: 'arb_phylo &'] arb_phylo: error while loading shared libraries: libXm.so.3: cannot open shared object file: No such file or directory

[guest]

Finally this did the trick:

sudo ln -s /usr/lib/libXm.so.4.0.3 /usr/lib/libXm.so.3

Now everything works fine:

[Action: 'arb_phylo &']

[epruesse]

The newer versions of Ubuntu include openmotif 4 (libmotif4 package) instead of version 3. For ARB this does not matter, but the library dependency is still fixed at compile time, so ARB binaries built on older systems will require the .so.3 link. (Not entirely safe, but it's very unlikely that more than broken display/crashes would happen).

[guest]

Not sure what's going on, but after rebooting the system the error is back: starting arb:

/usr/bin/arb '

Create SAI Using . . > Filter by Base Frequency

[Action: 'arb_phylo &'] sh: 1: arb_phylo: not found

can't repeat my previous action, since the link is created already: sudo ln -s /usr/lib/libXm.so.4.0.3 /usr/lib/libXm.so.3

ln: failed to create symbolic link `/usr/lib/libXm.so.3': File exists

[epruesse]

Could you launch an xterm from within ARB and post the output from env and ldd $ARBHOME/bin/arb_phylo? (From env only ARBHOME, PATH, LD_LIBRARY_PATH are really needed)

[guest]

Thanks sure:

env ARBHOME=/usr/lib/arb PATH=/usr/lib/arb/bin LD_LIBRARY_PATH=/usr/lib/arb/lib: . . . .

ldd $ARBHOME/bin/arb_phylo ldd: ldd usr/lib/arb/bin/arb_phylo: No such file or directory

I typed that in here, since I didn't find a way to copy from the xterm window.

[epruesse]

Sounds a bit like the ARB installation provided with Biolinux is broken.

The command Ralf mentioned will start the ARB you installed:

export ARBHOME=/home/tv195/ARB; cd $ARBHOME; bin/arb