I've been using the ete2 module on very powerful servers for some time.
Everything was fine until it started going very slowly (one get_taxid_translator() function per minute), now I cannot even get past ncbi = NCBITaxa() assignment.
I have uninstalled and reinstalled anaconda2, tried updating to ete3, everything works fine on our 'development servers' but still cannot get past the ncbi = NCBITaxa() line in any piece of software on our normal servers. Even the following script fails to finish
#!/usr/bin/env python
from ete3 import NCBITaxa
ncbi = NCBITaxa()
print "Finished"
Has this happened to anyone else? Do I need to downgrade any dependencies? Could it be a permissions issue?
When I run the basic script ctrl+c nor ctrl+z will escape the script and I have to use kill -9 <job-id> to kill the script. If I wait too long the process enters an uninterruptible sleep.
Thank you in advance,
Alexis.
Python 2.7.12 :: Anaconda custom (64-bit)
gcc (GCC) 5.4.0
Related
I am trying to compile a python program to an executable application on Mac OS X (Catalina) using py2app, and just cannot get it to work at all, would greatly appreciate if anybody can point out what I'm doing wrong. For the purposes of debugging my py2app problems, I have simplfied my python program down to:
d = 0.1
print ("starting")
for a in range (100000000):
d = d + 0.1
print ("finishing")
which is meant to print "starting" to the console, run for a while (about 10s on my Mac), and then print ("finishing") and terminate. When I run the program from the command line it works fine. When I compile using py2app and then try to run the final compiled app, I am not getting it to do anything, no pulse, no signs of life - it just looks as if it's opening, and then nothing. (I have similar lack of luck when I replace the print statements with file writes)
To compile my program I am using what I found on the main py2app docs:
rm -rf build dist
py2applet --make-setup test_py2app.py
python3 setup.py py2app -A
after which py2app seems to finish normally without any error messages. As described above, though, when I double click the resulting application icon, it seems to open but nothing happens.
If it helps, when I open the Console window and search for all messages mentioning my app ("test_py2app") I get the following logs:
(which includes the ominous sounding "Death sentinel fired!" message a few messages up from the bottom. Note: all of this occurs with 0.2 seconds, far quicker than my app should take to run and terminate).
Thanks in advance.
I'm running Mac OSX 10.10, Yosemite, and am trying to set up an anacron job that runs a python script weekly.
My anacron tab is as follows:
# /etc/anacrontab
#period delay job-identifier command
7 10 cron.test /absolute/path/to/my/doc/test.py
Nothing happens when I run sudo anacron -fn, and no timestamp file is created when I run anacron -u. The python script is executable, and I've included #!/usr/bin/env python at the top. How can I fix this and get anacron to run?
P.S. - As an aside, I would prefer not to use launchd. What kind of program accepts its inputs in a pseudo-XML format in 2017??
It seems that anacron is no longer available for macOS, or never was at all according to this comment: https://apple.stackexchange.com/a/227308/176514
I'm afraid you may need to take a look at launchd. More about that here:
How do I set a task to run every so often?
EDIT:
After some searching, it seems that this link has the latest version, made for 10.4 Tiger. I'm not sure that will work with Yosemite, but it is worth a shot.
https://web.archive.org/web/20100723043612/http://members.cox.net/18james/anacron-tiger.html
I installed python 2.7.10 on my 1and1 linux hosting service about 8 months ago (using instructions from http://geeksta.net/geeklog/python-shared-hosting/) and everything was working fine (I had a daily cron job that would call my python script). But recently,my python script stopped working and it appears that the call to python itself is the culprit, rather than the python code. Whenever I type 'python' into the command line in the 1and1 unix ssh session now, i get the following error message
"-bash: /kunden/homepages/26/xxxxxxxxxx/htdocs/python27/bin/python: No
such file or directory"
It's been awhile since I installed things, but I don't believe I had this issue previously. I'm trying to figure out why it's not working and what I can do to get it fixed. It appears that calling python isn't working properly (which would affect my script as well).
Any help with getting this working would be greatly appreciated.
when you type python, system find it in /kunden/homepages/26/xxxxxxxxxx/htdocs/python27/bin/python, but there is no such a file in fact.
what you need to do is trying to locate your python binary executable file, and alias your python to your file
I ended up just reinstalling python 2.7 again and it works again. Not sure why it stopped working before.
Now I can type "python" in the command line and it starts the Python console.
Greetings dear community,
I am currently using Sublime Text 2 (Unregistered) as my coding agent. And there is a strange behavior i noticed lately. When i am running a code in sublime text(Through build, with CTRL-B), if a code needs long time to run, like an infinite loop, I try to cancel the build(I specified CTRL-SHIFT-B to cancel build), sublime text shows me a message that build is cancelled
[Cancelled]
like so. In regular command line this means python program is no longer running. As I think it should be the same in sublime text, however, it is not. As longer i keep trying to cancel than build again, more and more python.exe keeps showing in the task manager. I can have like 10 python.exe running behind if I don't end process manually through task manager. Can somebody explain this behavior to me please ? And the reason behind it, can I prevent it ?
By the way, I tested the Python IDLE, and command prompt before asking so i could provide more information
Python IDLE shows same behavior and keeps python exe's running after cancelling.
Command prompt stops the process with no problem.
I am using python2 in a windows 8.1 system.
Thanks in advance for your time.
I'm running NPP 6.3.1 (UNICODE) and the current pythonscript plugin (python 2.7.6, pythonscript 0.9.2.0)
I recently got a new machine and had to reinstall both NPP and PythonScript (PS). I wrote a basic script a little while ago and had been using it a good bit and it worked fine using the PS plugin.
I installed everything and run the script through the PS plugin menu but nothing happens. I try it again and now, I keep getting the following error:
Another script is currently running. Running two scripts at the same time could produce unpredictable results, and therefore is disabled.
The script is designed to search the document and find the next available point number and insert it at the cursor. Like I said, it's a simple script that has a defined start and end. I've never had a problem with it before. So, I decided to create a new script (test.py) which consists entirely of the following:
console.write("test")
Nothing. The console doesn't show any activity no matter what I do, which leads me to believe that the script isn't even starting, even though it says that it loads up (in 16ms) and says its ready...
I tried uninstalling everything and reinstalling but still nothing. I haven't tried previous versions yet.
Am I missing something stupid?
The problem was that I did not have the most current version. After installing version 6.6.6 and PythonScript 1.0.2, it works.
Just want to leave this information for the next people who come in with this problem.