i had meet a problem when i run snakemake in cluster system, "missingoutputfile" and i had searched trying to solve the problem, maybe because it is "run" derived, not "shell", and it is a bug, in the new verision you had solve this problem, when i update it (verison 5.32.0). but another problem is raising up.
Error in rule predict_plasforest:
jobid: 34
output: linear_plasmid_genome/DP-Sample058-S54-adapter-phix-moving-sickle-sss_contigs_1kb.csv
log: log/isolating-linear-contig/DP-Sample058-S54-adapter-phix-moving-sickle-sss_linear_plasforest.out, log/isolating-linear-contig/DP-Sample058-S54-adapter-phix-moving-sickle-sss_linear_plasforest.err (check log file(s) for error message)
conda-env: /home/projects/ku_00041/apps/wanli/F_pipeline/conda_envs/60d0848d
shell:
export PATH=$PATH:/home/projects/ku_00041/apps/wanli/F_pipeline/db/blast/bin;cp /home/projects/ku_00041/apps/wanli/F_pipeline/db/plasforest/plasmid_refseq.* .;cp /home/projects/ku_00041/apps/wanli/F_pipeline/db/plasforest/plasforest.sav .;python3 /home/projects/ku_00041/apps/wanli/F_pipeline/db/plasforest/PlasForest.py -i assmebly_res/DP-Sample058-S54-adapter-phix-moving-sickle-sss_contigs_1kb.fasta -r -b -f --threads 30 -o linear_plasmid_genome/DP-Sample058-S54-adapter-phix-moving-sickle-sss_contigs_1kb.csv 2>log/isolating-linear-contig/DP-Sample058-S54-adapter-phix-moving-sickle-sss_linear_plasforest.err >log/isolating-linear-contig/DP-Sample058-S54-adapter-phix-moving-sickle-sss_linear_plasforest.out
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
cluster_jobid: 30135295
when i see the log file:
Traceback (most recent call last):
File "/home/projects/ku_00041/apps/wanli/F_pipeline/db/plasforest/PlasForest.py", line 26, in <module>
from sklearn.ensemble import RandomForestClassifier
ModuleNotFoundError: No module named 'sklearn'
but in the conda-env, it has already install sklean. and when i activate this env and reun the same command, it is working.
did you know how to solve this problem?
Related
everyone i'm using oracle arm/amd processor servers with ubuntu 22.04
i have searching for an solution for this over 1 week more than 100 hours
but i had no luck to figure out what is the problem
so if you know about this please help me!
what is problem :
here's a simply code with pyperclip
import pyperclip
string = 'testing'
pyperclip.copy(string)
a = pyperclip.paste()
print()
whenever i execute this code directly in the cli , it is okay to run
However whenever i run this code with schedulers like Crontab or Systemd.timer
(xclip && xsel is already installed)
i got this error and cannot run the code like below
Traceback (most recent call last):
File "/home/ubuntu/web_selenium/pytest.py", line 10, in <module>
pyperclip.copy(string)
File "/usr/lib/python3/dist-packages/pyperclip/__init__.py", line 689, in lazy_load_stub_copy
return copy(text)
File "/usr/lib/python3/dist-packages/pyperclip/__init__.py", line 358, in __call__
raise PyperclipException(EXCEPT_MSG)
pyperclip.PyperclipException:
Pyperclip could not find a copy/paste mechanism for your system.
For more information, please visit https://pyperclip.readthedocs.io/en/latest/index.html#not-implemented-error
i tried most of solutions in stackoverflow, mostly it was about setting path for interpreter and packages
of course i installed xclip and xsel as well / everything is good when i run code directly through cli
but only when i run code or shell script through Crontab , Systemd.timer, this error is generated
what i have tried
1. run pyperclip code through shell script with various python env PATH
i tried to lay all the possible env path like /usr/bin:/usr/local/bin .......
and even my python pakages path as .profile and ~./bashrc - failed
2. set new venv and install all the modules, run code - failed
3. run crontab as root - failed
4. install new ubuntu and switch server ubuntu amd -> ubuntu aarch64 - failed
5. reinstall module - failed
6. set shebang inside of python script ( whereis python3 - inside of python file - #!/usr/bin/python3.10) - failed
7. set shell into crontab (SHELL=/bin/bash) - failed
now i'm thinking this is the problem of pyperclip
pleaese help me!
I have an scp function as follows:
def scp_to38():
child = pexpect.spawn(f"scp {tar_file_path} bbmprd#10.82.20.38:/app2/upload/")
child.expect(f"bbmprd#10.82.20.38's password:")
child.sendline("password")
child.interact()
print(f'{tar_file_path} SENT TO 38:/app2/upload/')
and it is throwing me an error saying a problem with child.interact()
Traceback (most recent call last):
File "scan_for_upload.py", line 39, in <module>
scp_to38()
File "scan_for_upload.py", line 26, in scp_to38
child.interact()
File "/app/anaconda3/envs/python37-1/lib/python3.7/site-packages/pexpect/pty_spawn.py", line 788, in interact
mode = tty.tcgetattr(self.STDIN_FILENO)
termios.error: (25, 'Inappropriate ioctl for device')
I am running the script in a nohup process, I believe that is causing this issue. Because when I run the script in the console, it works fine. How do I interact with the scp password in a nohup process using pexpect module? (I can't install any other external modules in my environment)
interact() is for manual interaction with the spawned process and it requires to be running on a tty but nohup provides no tty. You can just replace child.interact() with child.expect(pexpect.EOF, timeout=None).
I am trying to use kaggle command line tool and I am running into problems with using it inside my own vm. I downloaded the API token from the site and placed it in /.kaggle/kaggle.json on windows. My vm has ubuntu installed and in the Vagrant file I have the following:
config.vm.synced_folder ENV['HOME'] + "/.kaggle", "/home/ubuntu/.kaggle", mount_options: ['dmode=700,fmode=700']
config.vm.provision "shell", inline: <<-SHELL
echo "export KAGGLE_CONFIG_DIR='/home/ubuntu/.kaggle/kaggle.json'" >> /etc/profile.d/myvar.sh
SHELL
when running env command in the vm I see it is correct:
KAGGLE_CONFIG_DIR=/home/ubuntu/.kaggle/kaggle.json
However, when I try to use the kaggle command for example kaggle -h I get the the following
(main) vagrant#dev:/home/ubuntu/.kaggle$ ls
kaggle.json
(main) vagrant#dev:/home/ubuntu/.kaggle$ kaggle -h
Traceback (most recent call last):
File "/user/home/venvs/main/bin/kaggle", line 5, in <module>
from kaggle.cli import main
File "/user/home/venvs/main/lib/python3.7/site-packages/kaggle/__init__.py", line 23, in <module>
api.authenticate()
File "/user/home/venvs/main/lib/python3.7/site-packages/kaggle/api/kaggle_api_extended.py", line 149, in authenticate
self.config_file, self.config_dir))
OSError: Could not find kaggle.json. Make sure it's located in /home/ubuntu/.kaggle/kaggle.json. Or use the environment method.
The paths are all correct and the file is where it should be looking for it. Anyone know what the issue could be? Is it because it is mounted?
Alright, I misread the instructions: "You can define a shell environment variable KAGGLE_CONFIG_DIR to change this location to $KAGGLE_CONFIG_DIR/kaggle.json"
So the env variable should be /home/ubuntu/.kaggle/ instead of /home/ubuntu/.kaggle/kaggle.json.
SSH into a VOLTTRON instance, installing agents works. Log out, log back in and installing results in the following error:
2016-09-13 11:46:24,409 () volttron.platform.vip.agent.subsystems.rpc ERROR: unhandled exception in JSON-RPC method 'install_agent':
Traceback (most recent call last):
File "/home/volttron/volttron/volttron/platform/vip/agent/subsystems/rpc.py", line 168, in method
return method(*args, **kwargs)
File "/home/volttron/volttron/volttron/platform/control.py", line 287, in install_agent
agent_uuid = self._aip.install_agent(path, vip_identity=vip_identity)
File "/home/volttron/volttron/volttron/platform/aip.py", line 296, in install_agent
unpack(agent_wheel, dest=agent_path)
File "/home/volttron/volttron/env/local/lib/python2.7/site-packages/wheel/tool/__init__.py", line 135, in unpack
sys.stderr.write("Unpacking to: %s\n" % (destination))
IOError: [Errno 5] Input/output error
When any background process is disowned, the ssh session is terminated, stdeff and stdout are not redirected to /dev/null, and the process tries to write to either it results in an IOError.
In this case one of the third party libraries that VOLLTRON uses when installing an agent tries to write to stderr (much to our chagrin). Even if the platform is run with the -l option it will still occasionally write to stderr. Unfortunately there is no reliable way for VOLTTRON to do the right thing with stderr in all cases so we have to leave it up to the user to know when they need to redirect output to /dev/null.
To run in the background use start-stop-daemon which automatically redirects everything to /dev/null or use this command to start the platform:
volttron -vv -l volttron.log > /dev/null 2>&1&
You can then safely disown the process and logout. Installations will still work.
I have a self-hosted gitlab and I would like to install a package hosted there using ssh.
I tried:
pip install git+ssh://git#<my_domain>:se7entyse7en/<project_name>.git
Here's the output:
Downloading/unpacking git+ssh://git#<my_domain>:se7entyse7en/<project_name>.git
Cloning ssh://git#<my_domain>:se7entyse7en/<project_name>.git to /var/folders/3r/v7swlvdn2p7_wyh9wj90td2m0000gn/T/pip-4_JdRU-build
ssh: Could not resolve hostname <my_domain>:se7entyse7en: nodename nor servname provided, or not known
fatal: Could not read from remote repository.
Please make sure you have the correct access rights and the repository exists.
Update:
I tried to upload it on gitlab.com and after having uploaded the repo I tried to install it by running:
pip install git+ssh://git#gitlab.com:loumarvincaraig/<project_name>.git
but the nothing changed. In particular here's the content of pip.log:
/Users/se7entyse7en/Envs/test/bin/pip run on Mon Nov 17 22:14:51 2014
Downloading/unpacking git+ssh://git#gitlab.com:loumarvincaraig/<project_name>.git
Cloning ssh://git#gitlab.com:loumarvincaraig/<project_name>.git to /var/folders/3r/v7swlvdn2p7_wyh9wj90td2m0000gn/T/pip-91JVFi-build
Found command 'git' at '/usr/local/bin/git'
Running command /usr/local/bin/git clone -q ssh://git#gitlab.com:loumarvincaraig/<project_name>.git /var/folders/3r/v7swlvdn2p7_wyh9wj90td2m0000gn/T/pip-91JVFi-build
Complete output from command /usr/local/bin/git clone -q ssh://git#gitlab.com:loumarvincaraig/<project_name>.git /var/folders/3r/v7swlvdn2p7_wyh9wj90td2m0000gn/T/pip-91JVFi-build:
Cleaning up...
Command /usr/local/bin/git clone -q ssh://git#gitlab.com:loumarvincaraig/<project_name>.git /var/folders/3r/v7swlvdn2p7_wyh9wj90td2m0000gn/T/pip-91JVFi-build failed with error code 128 in None
Exception information:
Traceback (most recent call last):
File "/Users/se7entyse7en/Envs/test/lib/python2.7/site-packages/pip/basecommand.py", line 134, in main
status = self.run(options, args)
File "/Users/se7entyse7en/Envs/test/lib/python2.7/site-packages/pip/commands/install.py", line 236, in run
requirement_set.prepare_files(finder, force_root_egg_info=self.bundle, bundle=self.bundle)
File "/Users/se7entyse7en/Envs/test/lib/python2.7/site-packages/pip/req.py", line 1092, in prepare_files
self.unpack_url(url, location, self.is_download)
File "/Users/se7entyse7en/Envs/test/lib/python2.7/site-packages/pip/req.py", line 1231, in unpack_url
return unpack_vcs_link(link, loc, only_download)
File "/Users/se7entyse7en/Envs/test/lib/python2.7/site-packages/pip/download.py", line 410, in unpack_vcs_link
vcs_backend.unpack(location)
File "/Users/se7entyse7en/Envs/test/lib/python2.7/site-packages/pip/vcs/__init__.py", line 240, in unpack
self.obtain(location)
File "/Users/se7entyse7en/Envs/test/lib/python2.7/site-packages/pip/vcs/git.py", line 111, in obtain
call_subprocess([self.cmd, 'clone', '-q', url, dest])
File "/Users/se7entyse7en/Envs/test/lib/python2.7/site-packages/pip/util.py", line 670, in call_subprocess
% (command_desc, proc.returncode, cwd))
InstallationError: Command /usr/local/bin/git clone -q ssh://git#gitlab.com:loumarvincaraig/<project_name>.git /var/folders/3r/v7swlvdn2p7_wyh9wj90td2m0000gn/T/pip-91JVFi-build failed with error code 128 in None
I don't know why, but by running the following command it worked (slash instead of : after <my_domain>):
pip install git+ssh://git#<my_domain>/se7entyse7en/<project_name>.git
# ^
# slash instead of :
Yes. This is the default use:
pip install git+ssh://git#<my_domain>:22/<project_group>/<project_name>.git
The use of the colon by itself implies the default ssh port number 22. Because you can control the port number of your server, the port number could be different. Git enables customisation by not providing :22/ or / only.