command not found error for basic commands
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CK
Jun 8, 2012, 6:05:27 PM6/8/12
to Qiime Forum
I am running Qiime virtualbox 1.3.0, this is the first time using in a
few months. However, when inputting basic commands such as :
print_qiime_config.py
i get the following error:
qiime@localhost:~$ print_qiime_config.py
print_qiime_config.py: command not found
This is also true for the other commands such as: check_id_map.py,
and pick_otus_through_otu_table.py.
Why are none of the basic overview tutorial commands working?
few months. However, when inputting basic commands such as :
print_qiime_config.py
i get the following error:
qiime@localhost:~$ print_qiime_config.py
print_qiime_config.py: command not found
This is also true for the other commands such as: check_id_map.py,
and pick_otus_through_otu_table.py.
Why are none of the basic overview tutorial commands working?
Will Van Treuren
Jun 8, 2012, 6:31:22 PM6/8/12
to qiime...@googlegroups.com
Hi CK,
The commands are likely not working because you do not have qiime in
your path. If you open a terminal and type:
env
you will see a list of variables. Look through them for PATH and
PYTHONPATH. If your PATH variable doesnt include the path to wherever
your qiime scripts are stored then that is very likely the source of
your problem. If this is the case, all you need to do is update your
.bashrc file to include paths to the qiime scripts and library code.
Type:
vim ~/.bashrc
and then add these lines to the end of your profile.
export PATH=/path/to/qiime/scripts
export PYTHONPATH=/path/to/qiime/library_code
where the /path/to... above is the actual path to those files on your
system. For instance, if your parent qiime folder is /home/Qiime/,
then you would add:
export PATH=~/Qiime/scripts/
export PYTHONPATH=~/Qiime/
You might also find it helpful to download the latest qiime virtual
box (v1.5) as it has a bunch of new features and fixes and a clean
install is always exciting.
I hope this helps!
Will
The commands are likely not working because you do not have qiime in
your path. If you open a terminal and type:
env
you will see a list of variables. Look through them for PATH and
PYTHONPATH. If your PATH variable doesnt include the path to wherever
your qiime scripts are stored then that is very likely the source of
your problem. If this is the case, all you need to do is update your
.bashrc file to include paths to the qiime scripts and library code.
Type:
vim ~/.bashrc
and then add these lines to the end of your profile.
export PATH=/path/to/qiime/scripts
export PYTHONPATH=/path/to/qiime/library_code
where the /path/to... above is the actual path to those files on your
system. For instance, if your parent qiime folder is /home/Qiime/,
then you would add:
export PATH=~/Qiime/scripts/
export PYTHONPATH=~/Qiime/
You might also find it helpful to download the latest qiime virtual
box (v1.5) as it has a bunch of new features and fixes and a clean
install is always exciting.
I hope this helps!
Will
Will Van Treuren
Jun 8, 2012, 6:41:38 PM6/8/12
to qiime...@googlegroups.com
Hi CK,
You need to modify the commands I gave you in my last reply just a
bit. Instead of the:
export PATH=~/Qiime/scripts/
export PYTHONPATH=~/Qiime/
it needs to be:
export PATH=~/Qiime/scripts/:$PATH
export PYTHONPATH=~/Qiime/:$PATH
Also, here is the link to the download for the latests qiime virtual
machine - ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/QIIME-1.5.0-amd64.vdi.gz
Sorry about the confusion,
Will
You need to modify the commands I gave you in my last reply just a
bit. Instead of the:
export PATH=~/Qiime/scripts/
export PYTHONPATH=~/Qiime/
it needs to be:
export PATH=~/Qiime/scripts/:$PATH
export PYTHONPATH=~/Qiime/:$PATH
Also, here is the link to the download for the latests qiime virtual
machine - ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/QIIME-1.5.0-amd64.vdi.gz
Sorry about the confusion,
Will
CK
Jun 8, 2012, 6:44:53 PM6/8/12
to Qiime Forum
Hey Will, this is what I get when putting in env. How can I tell if
the PATH variable doesn't include the path to where
the qiime scripts are stored? Also, if I download the latest
virtualbox will this solve the problem? I am afraid to lose the data
that I produced in this old virtualbox. Thank you.
qiime@localhost:~$ env
ORBIT_SOCKETDIR=/tmp/orbit-qiime
SSH_AGENT_PID=1139
TERM=xterm
SHELL=/bin/bash
XDG_SESSION_COOKIE=670a719844fb5023711a7df74c64044d-1339194203.582090-1827509720
WINDOWID=25165827
VAPPIO_HOME=/opt
GNOME_KEYRING_CONTROL=/tmp/keyring-I5q06f
GTK_MODULES=canberra-gtk-module
USER=qiime
LD_LIBRARY_PATH=/home/qiime/qiime_software/python-2.7.1-release/lib/
PYRO_LOOKUP_FILE=/home/qiime/qiime_software/ampliconnoise-1.25-release/
Data/LookUp_E123.dat
LS_COLORS=rs=0:di=01;34:ln=01;36:hl=44;37:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.lzma=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.rar=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.
7z=01;31:*.rz=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.axa=00;36:*.oga=00;36:*.spx=00;36:*.xspf=00;36:
SSH_AUTH_SOCK=/tmp/keyring-I5q06f/ssh
DEFAULTS_PATH=/usr/share/gconf/gnome.default.path
SESSION_MANAGER=local/localhost:@/tmp/.ICE-unix/1023,unix/localhost:/
tmp/.ICE-unix/1023
USERNAME=qiime
XDG_CONFIG_DIRS=/etc/xdg/xdg-gnome:/etc/xdg
DESKTOP_SESSION=gnome
PATH=/home/qiime/qiime_software/r-2.12.0-release/bin:/home/qiime/
qiime_software/python-2.7.1-release/bin:/home/qiime/qiime_software/
cdhit-3.1-release/.:/home/qiime/qiime_software/rdpclassifier-2.2-
release/.:/home/qiime/qiime_software/uclust-1.2.22-release/.:/home/
qiime/qiime_software/muscle-3.8.31-release/.:/home/qiime/
qiime_software/fasttree-2.1.3-release/.:/home/qiime/qiime_software/
chimeraslayer-4.29.2010-release/ChimeraSlayer:/home/qiime/
qiime_software/chimeraslayer-4.29.2010-release/NAST-iEr:/home/qiime/
qiime_software/vienna-1.8.4-release/.:/home/qiime/qiime_software/
ampliconnoise-1.25-release/Scripts:/home/qiime/qiime_software/
ampliconnoise-1.25-release/bin:/home/qiime/qiime_software/
clearcut-1.0.9-release/.:/home/qiime/qiime_software/
cdbtools-10.11.2010-release/.:/bin:/usr/local/sbin:/usr/local/bin:/usr/
sbin:/usr/bin:/sbin:/opt/vappio-py/vappio/cli:$PATH
PWD=/home/qiime
GDM_KEYBOARD_LAYOUT=us
LANG=en_US.UTF-8
MANDATORY_PATH=/usr/share/gconf/gnome.mandatory.path
GDM_LANG=en_US.UTF-8
GDMSESSION=gnome
SPEECHD_PORT=7561
HOME=/home/qiime
SHLVL=1
GNOME_DESKTOP_SESSION_ID=this-is-deprecated
LOGNAME=qiime
PYTHONPATH=/home/qiime/qiime_software/numpy-1.5.1-release/lib/
python2.7/site-packages:/home/qiime/qiime_software/MySQL-python-1.2.3-
release/lib/python2.7/site-packages:/home/qiime/qiime_software/
mpi4py-1.2.2-release/lib/python2.7/site-packages:/home/qiime/
qiime_software/lxml-2.2.7-release/lib/python2.7/site-packages:/home/
qiime/qiime_software/setuptools-0.6c11-release/lib/python2.7/site-
packages:/home/qiime/qiime_software/biom-format-0.9.1-release/python-
code/:/home/qiime/qiime_software/SQLAlchemy-0.7.1-release/lib/
python2.7/site-packages:/home/qiime/qiime_software/sphinx-1.0.4-
release/lib/python2.7/site-packages:/opt/vappio-twisted:/opt/vappio-py
XDG_DATA_DIRS=/usr/share/gnome:/usr/local/share/:/usr/share/
DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-
WvGa00fCCc,guid=fc8aedcbf25c2521d3b545494fd27b5d
SEQ_LOOKUP_FILE=/home/qiime/qiime_software/ampliconnoise-1.25-release/
Data/Tran.dat
LESSOPEN=| /bin/lesspipe %s
RDP_JAR_PATH=/home/qiime/qiime_software/rdpclassifier-2.2-release/
rdp_classifier-2.2.jar
DISPLAY=:0.0
LESSCLOSE=/bin/lesspipe %s %s
XAUTHORITY=/var/run/gdm/auth-for-qiime-PMWT9i/database
COLORTERM=gnome-terminal
_=/usr/bin/env
Will Van Treuren
Jun 8, 2012, 7:14:52 PM6/8/12
to qiime...@googlegroups.com
Hi CK,
It looks like the Qiime scripts are not actually in your path and the libraries are not in your pythonpath. I am not sure what the actual structure of your directories are. You should have something in /home/qiime/qiime_software/ that looks like qiime-1.3.0 (the numbers or name might be a little different).
It looks like the Qiime scripts are not actually in your path and the libraries are not in your pythonpath. I am not sure what the actual structure of your directories are. You should have something in /home/qiime/qiime_software/ that looks like qiime-1.3.0 (the numbers or name might be a little different).
Once you have located the above folder, check to see if it contains a bunch of folders with names like 'scripts', 'tests' etc. If it doesn't, it should contain only one folder called 'Qiime' or 'qiime'. Check inside this folder to see if this is where 'scripts' and 'tests' are. Whatever the folder where scripts and tests is located is the folder we need. If its actually called qiime-1.3.0/ then here is how you must change your .bashrc file. Open .bashc up in vim or a text editor, whatever you are comfortable with.
The end of the line that says PATH should look something like - opt/vappio-py/vappio/cli:$PATH. You need to insert /home/qiime/qiime_software/qiime-1.3.0/scripts/: between the cli: and $PATH, so it would look like: opt/vappio-py/vappio/cli:/home/qiime/qiime_software/qiime-1.3.0/scripts/:$PATH (you need to add a colon before $PATH as well).
The end of the line that says PYTHONPATH should look something like - :/opt/vappio-twisted:/opt/vappio-py. Just add :/home/qiime/qiime_software/qiime-1.3.0/ so it would look like:
:/opt/vappio-twisted:/opt/vappio-py:/home/qiime/qiime_software/qiime-1.3.0/
:/opt/vappio-twisted:/opt/vappio-py:/home/qiime/qiime_software/qiime-1.3.0/
Save the changes, open a new terminal, and try print_qiime_config.py. If it works then we have solved the problem. If not, send me a copy of your .bashrc file and a list of the directories that are in /home/qiime/qiime_software/ (can just copy and paste the results of ls while in that directory).
CK
Jun 9, 2012, 6:32:28 PM6/9/12
to Qiime Forum
Hi Will, I cant find the folder with Qiim 1.3.0. This is what I have
when finding it in unix:
qiime@localhost:~$ cd / qiime software
qiime@localhost:/$ ls
bin home lib64 opt selinux tmp vmlinuz.old
boot initrd.img lost+found proc software usr
dev initrd.img.old media root srv var
etc lib mnt sbin sys vmlinuz
This is what I find when oppening software folder in the window:
/software/ampliconnoise-1.25-release
/software/blast-2.2.22-release
/software/cdbtools-10.11.2010-release
/software/chimeraslayer-4.29.2010-release
/software/clearcut-1.0.9-release
/software/cytoscape-2.7.0-release
/software/fasttree-2.1.3-release
/software/gg_otus-4feb2011-release
/software/infernal-1.0.2-release
/software/mothur-1.6-release
/software/python-2.7.1-release
/software/r-2.12.0-release
/software/raxml-7.0.3-release
/software/vienna-1.8.4-release
/software/core_set_aligned.fasta.imputed
/software/lanemask_in_1s_and_0s
Also, when I type vim ~/.bashrc, I get this message:
E325: ATTENTION
Found a swap file by the name "~/.bashrc.swp"
owned by: qiime dated: Fri Jun 8 22:37:12 2012
file name: ~qiime/.bashrc
modified: YES
user name: qiime host name: localhost
process ID: 1611
While opening file "/home/qiime/.bashrc"
dated: Fri Jun 8 20:40:52 2012
(1) Another program may be editing the same file.
If this is the case, be careful not to end up with two
different instances of the same file when making changes.
Quit, or continue with caution.
(2) An edit session for this file crashed.
If this is the case, use ":recover" or "vim -r /home/
qiime/.bashrc"
to recover the changes (see ":help recovery").
If you did this already, delete the swap file "/home/
qiime/.bashrc.swp"
to avoid this message.
Swap file "~/.bashrc.swp" already exists!
[O]pen Read-Only, (E)dit anyway, (R)ecover, (D)elete it, (Q)uit,
(A)bort:
Can you tell me, If I install 1.5.0 virtualbox, will it be a separate
system from 1.3.0, that is will I still have 1.3.0 virtualbox with all
of the data I worked on before.
> opt/vappio-py/vappio/cli:/home/qiime/qiime_software/qiime-1.3.0/scripts/:$PATH
> * (you need to add a colon before $PATH as well).
> *
> *
> *
>
> 7z=01;31:*.rz=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.axa=00;36:*.oga=00;36:*.spx=00;36:*.xspf=00;36:
when finding it in unix:
qiime@localhost:~$ cd / qiime software
qiime@localhost:/$ ls
bin home lib64 opt selinux tmp vmlinuz.old
boot initrd.img lost+found proc software usr
dev initrd.img.old media root srv var
etc lib mnt sbin sys vmlinuz
This is what I find when oppening software folder in the window:
/software/ampliconnoise-1.25-release
/software/blast-2.2.22-release
/software/cdbtools-10.11.2010-release
/software/chimeraslayer-4.29.2010-release
/software/clearcut-1.0.9-release
/software/cytoscape-2.7.0-release
/software/fasttree-2.1.3-release
/software/gg_otus-4feb2011-release
/software/infernal-1.0.2-release
/software/mothur-1.6-release
/software/python-2.7.1-release
/software/r-2.12.0-release
/software/raxml-7.0.3-release
/software/vienna-1.8.4-release
/software/core_set_aligned.fasta.imputed
/software/lanemask_in_1s_and_0s
Also, when I type vim ~/.bashrc, I get this message:
E325: ATTENTION
Found a swap file by the name "~/.bashrc.swp"
owned by: qiime dated: Fri Jun 8 22:37:12 2012
file name: ~qiime/.bashrc
modified: YES
user name: qiime host name: localhost
process ID: 1611
While opening file "/home/qiime/.bashrc"
dated: Fri Jun 8 20:40:52 2012
(1) Another program may be editing the same file.
If this is the case, be careful not to end up with two
different instances of the same file when making changes.
Quit, or continue with caution.
(2) An edit session for this file crashed.
If this is the case, use ":recover" or "vim -r /home/
qiime/.bashrc"
to recover the changes (see ":help recovery").
If you did this already, delete the swap file "/home/
qiime/.bashrc.swp"
to avoid this message.
Swap file "~/.bashrc.swp" already exists!
[O]pen Read-Only, (E)dit anyway, (R)ecover, (D)elete it, (Q)uit,
(A)bort:
Can you tell me, If I install 1.5.0 virtualbox, will it be a separate
system from 1.3.0, that is will I still have 1.3.0 virtualbox with all
of the data I worked on before.
> It looks like the Qiime scripts are not actually in your path and the
> libraries are not in your pythonpath. I am not sure what the actual
> structure of your directories are. You should have something in
> /home/qiime/qiime_software/ that looks like qiime-1.3.0 (the numbers or
> name might be a little different).
> Once you have located the above folder, check to see if it contains a bunch
> of folders with names like 'scripts', 'tests' etc. If it doesn't, it should
> contain only one folder called 'Qiime' or 'qiime'. Check inside this folder
> to see if this is where 'scripts' and 'tests' are. Whatever the folder
> where scripts and tests is located is the folder we need. If its actually
> called qiime-1.3.0/ then here is how you must change your .bashrc file.
> Open .bashc up in vim or a text editor, whatever you are comfortable with.
> The end of the line that says PATH should look something like -
> opt/vappio-py/vappio/cli:$PATH. You need to insert
> /home/qiime/qiime_software/qiime-1.3.0/scripts/: between the cli: and
> $PATH, so it would look like: *
> libraries are not in your pythonpath. I am not sure what the actual
> structure of your directories are. You should have something in
> /home/qiime/qiime_software/ that looks like qiime-1.3.0 (the numbers or
> name might be a little different).
> Once you have located the above folder, check to see if it contains a bunch
> of folders with names like 'scripts', 'tests' etc. If it doesn't, it should
> contain only one folder called 'Qiime' or 'qiime'. Check inside this folder
> to see if this is where 'scripts' and 'tests' are. Whatever the folder
> where scripts and tests is located is the folder we need. If its actually
> called qiime-1.3.0/ then here is how you must change your .bashrc file.
> Open .bashc up in vim or a text editor, whatever you are comfortable with.
> The end of the line that says PATH should look something like -
> opt/vappio-py/vappio/cli:$PATH. You need to insert
> /home/qiime/qiime_software/qiime-1.3.0/scripts/: between the cli: and
> opt/vappio-py/vappio/cli:/home/qiime/qiime_software/qiime-1.3.0/scripts/:$PATH
> * (you need to add a colon before $PATH as well).
> The end of the line that says PYTHONPATH should look something like -
> :/opt/vappio-twisted:/opt/vappio-py. Just add
> :/home/qiime/qiime_software/qiime-1.3.0/
> so it would look like:
> *:/opt/vappio-twisted:/opt/vappio-py:/home/qiime/qiime_software/qiime-1.3.0/
> :/opt/vappio-twisted:/opt/vappio-py. Just add
> :/home/qiime/qiime_software/qiime-1.3.0/
> so it would look like:
> *
> *
> *
> Save the changes, open a new terminal, and try print_qiime_config.py. If it
> works then we have solved the problem. If not, send me a copy of your
> .bashrc file and a list of the directories that are
> in /home/qiime/qiime_software/ (can just copy and paste the results of ls
> while in that directory).
>
> Will
>
> works then we have solved the problem. If not, send me a copy of your
> .bashrc file and a list of the directories that are
> in /home/qiime/qiime_software/ (can just copy and paste the results of ls
> while in that directory).
>
> Will
>
> On Fri, Jun 8, 2012 at 4:44 PM, CK <chen.calvi...@gmail.com> wrote:
>
> > Hey Will, this is what I get when putting in env. How can I tell if
> > the PATH variable doesn't include the path to where
> > the qiime scripts are stored? Also, if I download the latest
> > virtualbox will this solve the problem? I am afraid to lose the data
> > that I produced in this old virtualbox. Thank you.
>
> > qiime@localhost:~$ env
> > ORBIT_SOCKETDIR=/tmp/orbit-qiime
> > SSH_AGENT_PID=1139
> > TERM=xterm
> > SHELL=/bin/bash
>
> XDG_SESSION_COOKIE=670a719844fb5023711a7df74c64044d-1339194203.582090-1827509720> WINDOWID=25165827
>
> > Hey Will, this is what I get when putting in env. How can I tell if
> > the PATH variable doesn't include the path to where
> > the qiime scripts are stored? Also, if I download the latest
> > virtualbox will this solve the problem? I am afraid to lose the data
> > that I produced in this old virtualbox. Thank you.
>
> > qiime@localhost:~$ env
> > ORBIT_SOCKETDIR=/tmp/orbit-qiime
> > SSH_AGENT_PID=1139
> > TERM=xterm
> > SHELL=/bin/bash
>
> > VAPPIO_HOME=/opt
> > GNOME_KEYRING_CONTROL=/tmp/keyring-I5q06f
> > GTK_MODULES=canberra-gtk-module
> > USER=qiime
> > LD_LIBRARY_PATH=/home/qiime/qiime_software/python-2.7.1-release/lib/
> > PYRO_LOOKUP_FILE=/home/qiime/qiime_software/ampliconnoise-1.25-release/
> > Data/LookUp_E123.dat
>
> LS_COLORS=rs=0:di=01;34:ln=01;36:hl=44;37:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.lzma=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.rar=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.
> > GNOME_KEYRING_CONTROL=/tmp/keyring-I5q06f
> > GTK_MODULES=canberra-gtk-module
> > USER=qiime
> > LD_LIBRARY_PATH=/home/qiime/qiime_software/python-2.7.1-release/lib/
> > PYRO_LOOKUP_FILE=/home/qiime/qiime_software/ampliconnoise-1.25-release/
> > Data/LookUp_E123.dat
>
>
> 7z=01;31:*.rz=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.axa=00;36:*.oga=00;36:*.spx=00;36:*.xspf=00;36:
Jose Navas
Jun 9, 2012, 6:59:10 PM6/9/12
to qiime...@googlegroups.com
Hi CK,
qiime@localhost:~$ cd / qiime software
qiime@localhost:/$ ls
bin home lib64 opt selinux tmp vmlinuz.old
boot initrd.img lost+found proc software usr
dev initrd.img.old media root srv var
etc lib mnt sbin sys vmlinuz
you have spaces in your cd command. Hence, you are not changing to the qiime_software folder. the wight command is:
cd ~/qiime_software
Then, send us the output of the ls command.
Also, when I type vim ~/.bashrc, I get this message:
E325: ATTENTION
Found a swap file by the name "~/.bashrc.swp"
owned by: qiime dated: Fri Jun 8 22:37:12 2012
file name: ~qiime/.bashrc
modified: YES
user name: qiime host name: localhost
process ID: 1611
While opening file "/home/qiime/.bashrc"
dated: Fri Jun 8 20:40:52 2012
(1) Another program may be editing the same file.
If this is the case, be careful not to end up with two
different instances of the same file when making changes.
Quit, or continue with caution.
(2) An edit session for this file crashed.
If this is the case, use ":recover" or "vim -r /home/
qiime/.bashrc"
to recover the changes (see ":help recovery").
If you did this already, delete the swap file "/home/
qiime/.bashrc.swp"
to avoid this message.
Swap file "~/.bashrc.swp" already exists!
[O]pen Read-Only, (E)dit anyway, (R)ecover, (D)elete it, (Q)uit,
(A)bort:
This problem is caused because you have the file opened with other application.
Can you tell me, If I install 1.5.0 virtualbox, will it be a separate
system from 1.3.0, that is will I still have 1.3.0 virtualbox with all
of the data I worked on before.
Yes, If you install the 1.5.0 virtualbox is a separate system ( you will have two virtualboxes ). Your data will be on your 1.3.0 virtualbox.
Hope this helps!!!
Jose
CK
Jun 10, 2012, 1:25:09 AM6/10/12
to Qiime Forum
Hey Jose,
qiime@localhost:~$ cd ~/qiime_software
qiime@localhost:~/qiime_software$
qiime@localhost:~/qiime_software$ ls
activate.sh mpi4py-1.2.2-release
ampliconnoise-1.25-release muscle-3.8.31-release
biom-format-0.9.1-release MySQL-python-1.2.3-release
cdbtools-10.11.2010-release numpy-1.5.1-release
cdhit-3.1-release python-2.7.1-release
chimeraslayer-4.29.2010-release r-2.12.0-release
clearcut-1.0.9-release rdpclassifier-2.2-release
core_set_aligned.fasta.imputed setuptools-0.6c11-release
cytoscape-2.7.0-release sphinx-1.0.4-release
fasttree-2.1.3-release SQLAlchemy-0.7.1-release
lanemask_in_1s_and_0s uclust-1.2.22-release
lxml-2.2.7-release vienna-1.8.4-release
> > LS_COLORS=rs=0:di=01;34:ln=01;36:hl=44;37:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.lzma=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.rar=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.
>
> > 7z=01;31:*.rz=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.axa=00;36:*.oga=00;36:*.spx=00;36:*.xspf=00;36:
> ...
>
> read more »
qiime@localhost:~$ cd ~/qiime_software
qiime@localhost:~/qiime_software$
qiime@localhost:~/qiime_software$ ls
activate.sh mpi4py-1.2.2-release
ampliconnoise-1.25-release muscle-3.8.31-release
biom-format-0.9.1-release MySQL-python-1.2.3-release
cdbtools-10.11.2010-release numpy-1.5.1-release
cdhit-3.1-release python-2.7.1-release
chimeraslayer-4.29.2010-release r-2.12.0-release
clearcut-1.0.9-release rdpclassifier-2.2-release
core_set_aligned.fasta.imputed setuptools-0.6c11-release
cytoscape-2.7.0-release sphinx-1.0.4-release
fasttree-2.1.3-release SQLAlchemy-0.7.1-release
lanemask_in_1s_and_0s uclust-1.2.22-release
lxml-2.2.7-release vienna-1.8.4-release
>
> > 7z=01;31:*.rz=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.axa=00;36:*.oga=00;36:*.spx=00;36:*.xspf=00;36:
>
> read more »
Jose Navas
Jun 10, 2012, 12:14:58 PM6/10/12
to qiime...@googlegroups.com
Hi CK,
Your qiime folder is missing. I recommend that you install the qiime virtualbox 1.5.0 and then copy tha data from the old VB to the new one. Remember that you can use the Shared_Folder to copy the files faster.
Cheers,
CK
Jun 10, 2012, 5:55:13 PM6/10/12
to Qiime Forum
When I install 1.5.0 and run the open autorun prompt for adding guest
additions, I get the errors:
1)the header for the current running kernel were not found. If the
following module compilation fails then this could be the reason.
2)building the shared folder support module...fail
(look at /var/log/vboxadd-install.log to find out what went wrong)
3)warning: unknown version of the X windows system installed. Not
installing X window system drivers.
Building the main guest additions module and installing graphic
libraries and desktop services componenets were ok.
I cannot copy and paste from the virtualbox and the screen does not
maximize. Also I cannot copy anything to the shared folder and when I
type in :var/log/vboxadd-install.log to the terminal I
get :Permission denied. I have no idea where to find this r/log/
vboxadd-install.log, but I am going to guess that the error is from:
the header for the current running kernel were not found.
Can you tell me how to fix all of this so that it can run smoothly
like the previous virtualbox?
Also, on a different note, I have putty installed in another computer
and am supposed to be able to access Qiime from the system's unix
terminal there. What is the command for opening up Qiime in unix?
Thank you.
> > LS_COLORS=rs=0:di=01;34:ln=01;36:hl=44;37:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.lzma=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.rar=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.
>
> > 7z=01;31:*.rz=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.axa=00;36:*.oga=00;36:*.spx=00;36:*.xspf=00;36:
> ...
>
> read more »
additions, I get the errors:
1)the header for the current running kernel were not found. If the
following module compilation fails then this could be the reason.
2)building the shared folder support module...fail
(look at /var/log/vboxadd-install.log to find out what went wrong)
3)warning: unknown version of the X windows system installed. Not
installing X window system drivers.
Building the main guest additions module and installing graphic
libraries and desktop services componenets were ok.
I cannot copy and paste from the virtualbox and the screen does not
maximize. Also I cannot copy anything to the shared folder and when I
type in :var/log/vboxadd-install.log to the terminal I
get :Permission denied. I have no idea where to find this r/log/
vboxadd-install.log, but I am going to guess that the error is from:
the header for the current running kernel were not found.
Can you tell me how to fix all of this so that it can run smoothly
like the previous virtualbox?
Also, on a different note, I have putty installed in another computer
and am supposed to be able to access Qiime from the system's unix
terminal there. What is the command for opening up Qiime in unix?
Thank you.
> Your qiime folder is missing. I recommend that you install the qiime
> virtualbox 1.5.0 and then copy tha data from the old VB to the new one.
> Remember that you can use the Shared_Folder to copy the files faster.
>
> Cheers,
> Jose
>
> 2012/6/9 CK <chen.calvi...@gmail.com>
> virtualbox 1.5.0 and then copy tha data from the old VB to the new one.
> Remember that you can use the Shared_Folder to copy the files faster.
>
> Cheers,
> Jose
>
>
> > 7z=01;31:*.rz=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.axa=00;36:*.oga=00;36:*.spx=00;36:*.xspf=00;36:
>
> read more »
Antonio González Peña
Jun 11, 2012, 7:37:49 AM6/11/12
to qiime...@googlegroups.com
Hi CK,
Have you tried to running the installer using the command line vs the
autorun? The instructions from Before_you_start/1.Welcome.txt :
1. Release the mouse pointer from this Window using either the left
Command-key (Mac) or the right Control-key (Windows).
2. Go to the virtual box menu and select Devices->Install Guest
Additions... Click back into the virtual box, and then click 'Places'
on the menu bar. Select VBOXADDITIONS_4.0.2_69518. (Note the name
VBOXADDITIONS... may differ depending on your version of VirtualBox.)
A new window should appear in the virtual machine. Hit Open Autorun
Prompt.
3. Open a terminal by clicking on the black window with a > in the top
menu bar of the virtual machine, and paste this command into the
terminal:
sudo /media/VBOXADDITIONS_4.0.2_69518/VBoxLinuxAdditions.run
Again, the directory name VBOXADDITIONS... may differ depending on
your version of VirtualBox. You can run 'ls /media' to find the name
of this directory. When prompted, enter the password: qiime
4. When that command is finished running (i.e., you get a command
prompt back), restart the virtual machine by clicking the power button
to the right of word 'qiime' in the upper right corner of the virtual
machine window and then selecting 'Restart...'.
I'm assuming that you want to connect to your VM from another computer
using Putty, is this right? To do this you need to install the ssh
server, googling I found this good set of instructions:
http://www.liberiangeek.net/2011/04/enable-secure-shell-ssh-ubuntu-11-04-natty-narwhal/
Cheers
--
Antonio González Peña
Research Assistant, Knight Lab
University of Colorado at Boulder
https://chem.colorado.edu/knightgroup/
Have you tried to running the installer using the command line vs the
autorun? The instructions from Before_you_start/1.Welcome.txt :
1. Release the mouse pointer from this Window using either the left
Command-key (Mac) or the right Control-key (Windows).
2. Go to the virtual box menu and select Devices->Install Guest
Additions... Click back into the virtual box, and then click 'Places'
on the menu bar. Select VBOXADDITIONS_4.0.2_69518. (Note the name
VBOXADDITIONS... may differ depending on your version of VirtualBox.)
A new window should appear in the virtual machine. Hit Open Autorun
Prompt.
3. Open a terminal by clicking on the black window with a > in the top
menu bar of the virtual machine, and paste this command into the
terminal:
sudo /media/VBOXADDITIONS_4.0.2_69518/VBoxLinuxAdditions.run
Again, the directory name VBOXADDITIONS... may differ depending on
your version of VirtualBox. You can run 'ls /media' to find the name
of this directory. When prompted, enter the password: qiime
4. When that command is finished running (i.e., you get a command
prompt back), restart the virtual machine by clicking the power button
to the right of word 'qiime' in the upper right corner of the virtual
machine window and then selecting 'Restart...'.
I'm assuming that you want to connect to your VM from another computer
using Putty, is this right? To do this you need to install the ssh
server, googling I found this good set of instructions:
http://www.liberiangeek.net/2011/04/enable-secure-shell-ssh-ubuntu-11-04-natty-narwhal/
Cheers
Antonio González Peña
Research Assistant, Knight Lab
University of Colorado at Boulder
https://chem.colorado.edu/knightgroup/
CK
Jun 11, 2012, 10:59:28 AM6/11/12
to Qiime Forum
Hey,
Yes I did tried using the command line the results are the same.
Actually I meant just opening up qiime (from network administration)
that is preinstalled in unix, not my own virtualbox.
> server, googling I found this good set of instructions:http://www.liberiangeek.net/2011/04/enable-secure-shell-ssh-ubuntu-11...
> ...
>
> read more »
Yes I did tried using the command line the results are the same.
Actually I meant just opening up qiime (from network administration)
that is preinstalled in unix, not my own virtualbox.
>
> read more »
Antonio González Peña
Jun 11, 2012, 3:53:20 PM6/11/12
to qiime...@googlegroups.com
That is pretty strange, are you sure you selected Linux -> Ubuntu 64
when you created your virtual machine? If so can you try
re-downloading the image file and try again; I just did this and it
worked without a problem so my guess is that your image is corrupted.
Not sure what you are talking about, does the place that you work at
has a server with Qiime installed? If this is this the case you should
contact the admin of the machine for this information, if not can you
give us more background about your question?
when you created your virtual machine? If so can you try
re-downloading the image file and try again; I just did this and it
worked without a problem so my guess is that your image is corrupted.
Not sure what you are talking about, does the place that you work at
has a server with Qiime installed? If this is this the case you should
contact the admin of the machine for this information, if not can you
give us more background about your question?
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