gubbins would not run

[aphayt]

Dear Sir

I had a copy of Gubbins installed in BioLinux8 (Ubuntu 14.04). When I tried to run the program. I got:
yue@PC-027[yue] run_gubbins.py -h [ 1:03PM]
/home/yue/.linuxbrew/bin/run_gubbins.py: /home/yue/.linuxbrew/Cellar/gubbins/2.2.0/libexec/bin/run_gubbins.py: /home/yue/.linuxbrew/opt/python3/bin/python3.5: bad interpreter: No such file or directory
/home/yue/.linuxbrew/bin/run_gubbins.py: line 2: /home/yue/.linuxbrew/Cellar/gubbins/2.2.0/libexec/bin/run_gubbins.py: Success
It says success but it is not quite right as I could not run the program.

Please help,
Yue

[andrewjpage]

Hi Yue, From the error message it looks like Python is not setup correctly on your system. Try reinstalling python3 or contact your local system administrator for IT support. Regards, Andrew

…

On 21 February 2017 at 13:42, aphayt ***@***.***> wrote: Dear Sir I had a copy of Gubbins installed in BioLinux8 (Ubuntu 14.04). When I tried to run the program. I got: ***@***.***[yue] run_gubbins.py -h [ 1:03PM] /home/yue/.linuxbrew/bin/run_gubbins.py: /home/yue/.linuxbrew/Cellar/ gubbins/2.2.0/libexec/bin/run_gubbins.py: /home/yue/.linuxbrew/opt/python3/bin/python3.5: bad interpreter: No such file or directory /home/yue/.linuxbrew/bin/run_gubbins.py: line 2: /home/yue/.linuxbrew/Cellar/gubbins/2.2.0/libexec/bin/run_gubbins.py: Success It says success but it is not quite right as I could not run the program. Please help, Yue — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#187>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AABeV4vXte-AgxWPAdfv2K553IuiNuDCks5reunigaJpZM4MHVGu> .

[jb2cool]

The only thing I can see that's wrong is that LinuxBrew installed Python 3.6 where as the run_gubbins.py seems to be specifically calling Python 3.5. I have temporarily put in a symbolic link to redirect Python 3.5 to 3.6 and this seems to work but the LinuxBrew instructions seem to be broken as-is.

[aphayt]

Hi Andrew

Jason found LinuxBrew could not find Python 3.5 so he redirected to 3.6. When I tried Gubbins only I got:
yue@PC-027[CampyGubbins] /home/yue/.linuxbrew/bin/run_gubbins.py [12:25PM]
usage: run_gubbins.py [-h] [--outgroup OUTGROUP]
[--starting_tree STARTING_TREE] [--use_time_stamp]
[--verbose] [--no_cleanup] [--tree_builder TREE_BUILDER]
[--iterations ITERATIONS] [--min_snps MIN_SNPS]
[--filter_percentage FILTER_PERCENTAGE]
[--prefix PREFIX] [--threads THREADS]
[--converge_method CONVERGE_METHOD] [--version]
[--min_window_size MIN_WINDOW_SIZE]
[--max_window_size MAX_WINDOW_SIZE]
[--raxml_model RAXML_MODEL]
[--remove_identical_sequences]
alignment_filename
run_gubbins.py: error: the following arguments are required: alignment_filename
If I added fasta file as well, I got:
yue@PC-027[CampyGubbins] /home/yue/.linuxbrew/bin/run_gubbins.py 20ref10isolates.fa
../src/gubbins is not in your path

I could not find /src/... in the bin folder.

Many thanks,
Yue

[raymondkiu]

Hi Andrew

I have similar problem - could not run run_gubbins.py as common cannot be imported. I installed Gubbins through homebrew on my Mac. I suspect python 3.6 might be the issue?

Raymond

[JibrinLab]

Hi,
When I tried to run gubbins, I got this : run_gubbins.py
run_gubbins.py: command not found

But when I tried to reinstall I got this: Warning: linuxbrew/science/gubbins-2.2.0 already installed

Please help.

[jb2cool]

What does your $PATH variable look like? You you have the LinuxBrew bits in it?

[JibrinLab]

@jb2cool , sure I have LinuxBrew. I already had roary installed and it's a requirement. As for the path, do I still need to set any PATH? I am using a local Linux machine and I am the administrator.

[jb2cool]

I meant is LinuxBrew referenced in your $PATH variable.

If you just call the command run_gubbins.py then the OS needs to be able to find this script, the only way it can do this is if the script is in somewhere referenced by your $PATH variable.

You could try running the script by calling it via its absolute path, that would typically be something like;
/home/yourusername/.linuxbrew/bin/run_gubbins.py

[JibrinLab]

I got this message after running /home//.linuxbrew/bin/run_gubbins.py
: bash: /home//.linuxbrew/bin/run_gubbins.py: No such file or directory

[jb2cool]

Sorry, I corrected my thread, after the /hom and before the .linuxbrew you need to put your username. This is where LinuxBrew is installed for me, yours may be installed elsewhere.

[JibrinLab]

Thanks. I added my username. It gave me this result:

/home/osboxes/.linuxbrew/bin/run_gubbins.py
/home/osboxes/.linuxbrew/bin/run_gubbins.py: /home/osboxes/.linuxbrew/Cellar/gubbins/2.2.0/libexec/bin/run_gubbins.py: /home/osboxes/.linuxbrew/opt/python3/bin/python3.5: bad interpreter: No such file or directory
/home/osboxes/.linuxbrew/bin/run_gubbins.py: line 2: /home/osboxes/.linuxbrew/Cellar/gubbins/2.2.0/libexec/bin/run_gubbins.py: Success

I ran run_gubbins.py, still this result: run_gubbins.py: command not found

[aphayt]

I run my Gubbins from '/usr/bin/run_gubbins'. Note there is no py extension.

…

On Wed, Apr 5, 2017 at 12:21 PM, Jason Bramwell ***@***.***> wrote: Sorry, I corrected my thread, after the /hom and before the .linuxbrew you need to put your username. This is where LinuxBrew is installed for me, yours may be installed elsewhere. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#187 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AScC1EM9ZkrBwD5EdNEZRDHn7iNedOBNks5rs3kpgaJpZM4MHVGu> .

[JibrinLab]

@aphayt Oh thanks. My bad. Now it works without the py extension.

Thanks to @jb2cool too.

[jb2cool]

@ojonuba, that's exactly the same issue as Yue initially had when he opened this thread. Gubbins seems to be statically looking to Python 3.5 where as I suspect your LinuxBrew has installed a different version like Python 3.6

[raymondkiu]

@ojonuba @jb2cool does it mean the solution is to run run_gubbins without py extension?

[jb2cool]

@raymondkiu remember that your issue may be different to that of @ojonuba and @aphayt (Which seem to now be in the same place).

Since your issue seems to be importing the common module i'd first of all check that you can manually import this. Go into Python (Make sure you go into the right Python as the Mac probably has 2.7 installed by default) and try manually importing common

[JibrinLab]

@raymondkiu , try running it without the .py extension and see if it works for you. Otherwise you can post the error message here and someone will help respond. Best wishes.