hi guys can some one help me whit this pl
/usr/bin/wine: 40: exec: /usr/lib/wine/wine: Exec format error
Related
I'm creating a pipeline using snakemake to call methylation in nanopore sequencing data. I've run snakenake using the --dryrun option and the dag is constructed successfully. But when I add the option --profile slurm, I get the following error:
(nanopolish) [danielle.perley#talonhead2 nanopolish-CpG-calling]$ snakemake -np --use-conda --profile slurm test_data/20-001-002/20-001-002_fastq_pass.gz
Building DAG of jobs...
Job counts:
count jobs
1 combine_tech_reps
1
InputFunctionException in line 32 of /home/danielle.perley/nanopolish-CpG-calling/Snakefile:
Error:
SyntaxError: invalid syntax (<string>, line 1)
Wildcards:
sample=20-001-002
Traceback:
File "/home/danielle.perley/miniconda3/envs/nanopolish/lib/python3.7/site-packages/snakemake/executors/__init__.py", line 115, in run_jobs
File "/home/danielle.perley/miniconda3/envs/nanopolish/lib/python3.7/site-packages/snakemake/executors/__init__.py", line 120, in run
File "/home/danielle.perley/miniconda3/envs/nanopolish/lib/python3.7/site-packages/snakemake/executors/__init__.py", line 131, in _run
File "/home/danielle.perley/miniconda3/envs/nanopolish/lib/python3.7/site-packages/snakemake/executors/__init__.py", line 151, in printjob
File "/home/danielle.perley/miniconda3/envs/nanopolish/lib/python3.7/site-packages/snakemake/executors/__init__.py", line 137, in printjob
Line 33 is rule combine_tech_reps in my snakefile. (I'm only showing the first part of my snakefile here)
from snakemake.utils import validate
import pandas as pd
import os.path
import glob
configfile: "config.yaml"
samples_df = pd.read_table(config["samples"],sep = '\t')
samples_df = samples_df.set_index("Sample")
samples = list(samples_df.index.unique())
wildcard_constraints:
sample = "|".join(samples)
def get_fast5(wildcards):
f5 = glob.glob(os.path.join(config["raw_data"],wildcards.sample,"2*","fast5_pass"))
return(f5)
localrules: all,build_index
rule all:
input:
expand("results/Methylation/{sample}_frequency.tsv",sample=samples),
expand("results/alignments/{sample}_flagstat.txt",sample=samples),
expand("resources/QC/{sample}_pycoQC.json",sample=samples),
expand("results/QC/{sample}_pycoQC.html",sample=samples),
"report/multiQC.html"
rule combine_tech_reps:
input:
fqs = lambda wildcards: glob.glob(os.path.join(config["raw_data"],"{sample}","2*","{sample}_fastq_pass.gz").format(sample=wildcards.sample))
output:
fq = os.path.join(config["raw_data"],"{sample}","{sample}_fastq_pass.gz")
shell: """
zcat {input} > {output}
"""
I have a slurm profile file in the directory:
~/.config/snakemake/slurm/config.yaml
jobs: 10
cluster: "sbatch -p talon -t {resources.time} --mem={resources.mem} -c {resources.cpus} -o logs_slurm/{rule}_{wildcards} -e logs_slurm/{rule}_{wildcards}"
default-resources: [cpus=1, mem=2000, time=10:00]
use-conda: true
I'd really like to use this pipeline on our HPC, but I'm not sure what's causing this error.
I was able to solve my problem with the help of this post:
InputFunctionException: unexpected EOF while parsing
By adding the verbose flag:
snakemake -np --verbose --use-conda --profile slurm test_data/20-001-002/20-001-002_fastq_pass.gz
I could see that snakemake was having issues with the default resources:
10:00
^
Changing the default resources line of my config.yaml file:
default-resources: [cpus=1, mem=2000, time=600]
removed the error.
I am not sure if default-resources is a valid key in the config.
What happens if you try this as config.yaml:
jobs: 10
cluster: "sbatch -p talon -t {resources.time} --mem={resources.mem} -c {resources.cpus} -o logs_slurm/{rule}_{wildcards} -e logs_slurm/{rule}_{wildcards}"
use-conda: true
__default__:
time: 10
cpus: 1
mem: 2GB
running in python console: ( Windows)
>>> "C:\Users\xxxxx\Downloads\wget-1.11.4-1-bin\bin\wget.exe" google.com
File "<stdin>", line 1
"C:\Users\xxxxx\Downloads\wget-1.11.4-1-bin\bin\wget.exe" google.com
^
SyntaxError: invalid syntax
when I type mvim in my terminal it shows up something like this:
/usr/local/bin/mvim: line 31: import: command not found
/usr/local/bin/mvim: line 32: import: command not found
/usr/local/bin/mvim: line 37: flags: command not found
/usr/local/bin/mvim: line 38: -Wall,: command not found
/usr/local/bin/mvim: line 39: -Wextra,: command not found
/usr/local/bin/mvim: line 40: -Werror,: command not found
/usr/local/bin/mvim: line 41: -Wno-long-long,: command not found
/usr/local/bin/mvim: line 42: -Wno-variadic-macros,: command not found
/usr/local/bin/mvim: line 43: -fexceptions,: command not found
/usr/local/bin/mvim: line 44: -DNDEBUG,: command not found
/usr/local/bin/mvim: line 47: -DUSE_CLANG_COMPLETER,: command not found
/usr/local/bin/mvim: line 54: -std=c++11,: command not found
/usr/local/bin/mvim: line 59: -x,: command not found
/usr/local/bin/mvim: line 60: c++,: command not found
/usr/local/bin/mvim: line 61: -isystem,: command not found
/usr/local/bin/mvim: line 62: ../BoostParts,: No such file or directory
/usr/local/bin/mvim: line 63: -isystem,: command not found
/usr/local/bin/mvim: line 66:/System/Library/Frameworks/Python.framework/Headers,: No such file or directory
/usr/local/bin/mvim: line 67: -isystem,: command not found
/usr/local/bin/mvim: line 68: ../llvm/include,: No such file or directory
/usr/local/bin/mvim: line 69: -isystem,: command not found
/usr/local/bin/mvim: line 70: ../llvm/tools/clang/include,: No such file or directory
/usr/local/bin/mvim: line 71: -I,: command not found
/usr/local/bin/mvim: line 72: .,: command not found
/usr/local/bin/mvim: line 73: -I,: command not found
/usr/local/bin/mvim: line 74: ./ClangCompleter,: No such file or directory
/usr/local/bin/mvim: line 75: -isystem,: command not found
/usr/local/bin/mvim: line 76: ./tests/gmock/gtest,: No such file or directory
/usr/local/bin/mvim: line 77: -isystem,: command not found
/usr/local/bin/mvim: line 78: ./tests/gmock/gtest/include,: No such file or directory
/usr/local/bin/mvim: line 79: -isystem,: command not found
/usr/local/bin/mvim: line 80: ./tests/gmock,: No such file or directory
/usr/local/bin/mvim: line 81: -isystem,: command not found
/usr/local/bin/mvim: line 82: ./tests/gmock/include,: No such file or directory
/usr/local/bin/mvim: line 83: ]: command not found
/usr/local/bin/mvim: line 96: compilation_database_folder: command not found
/usr/local/bin/mvim: line 98: syntax error near unexpected token `compilation_database_folder'
/usr/local/bin/mvim: line 98: `if os.path.exists( compilation_database_folder ):'
thanks alot!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
I'm trying to Integrate Azure public cloud with Scalr and made some configuration changes like adding Azure "app_client_id, app_secret_key " in scalr-server.rb file. After saving this changes, i'm trying to run the reconfiguration command "sudo /opt/scalr-server/bin/scalr-server-ctl reconfigure" for reload/restart the services/components. But in doing so I ran into an error " Error executing action start on resource 'supervisor_service[service-analytics_poller]". So can any one from the other end help me out please.
Error Details :
RuntimeError
------------
Supervisor service service-analytics_poller was unable to be started
Cookbook Trace:
---------------
/opt/scalr-server/embedded/cookbooks/supervisor/providers/service.rb:49:in `block (2 levels) in class_from_file'
/opt/scalr-server/embedded/cookbooks/supervisor/providers/service.rb:47:in `block in class_from_file'
Resource Declaration:
---------------------
# In /opt/scalr-server/embedded/cookbooks/scalr-server/recipes/group_service_always_post.rb
5: supervisor_service name do
6: command "#{bin_dir_for node, 'service'}/scalrpy_proxy" \
7: " #{run_dir_for node, 'service'}/#{svc[:name]}.pid" \
8: " #{node[:scalr_server][:install_root]}/embedded/bin/python" \
9: " #{scalr_bundle_path node}/app/python/scalrpy/#{svc[:service_module]}.py" \
10: " --pid-file=#{run_dir_for node, 'service'}/#{svc[:name]}.pid" \
11: " --log-file=#{log_dir_for node, 'service'}/python-#{svc[:name]}.log" \
12: " --user=#{node[:scalr_server][:app][:user]}" \
13: " --group=#{node[:scalr_server][:app][:user]}" \
14: " --config=#{scalr_bundle_path node}/app/etc/config.yml" \
15: ' --verbosity=INFO' \
16: " #{svc[:service_extra_args]}" \
17: # Note: 'start' is added by the proxy.
18: stdout_logfile "#{log_dir_for node, 'supervisor'}/#{name}.log"
19: stderr_logfile "#{log_dir_for node, 'supervisor'}/#{name}.err"
20: autostart true
21: action [:enable, :start]
22: subscribes :restart, 'file[scalr_config]' if should_restart
23: subscribes :restart, 'file[scalr_code]' if should_restart
24: subscribes :restart, 'file[scalr_cryptokey]' if should_restart
25: subscribes :restart, 'file[scalr_id]' if should_restart
26: subscribes :restart, 'user[scalr_user]' if should_restart
27: end
28: end
Compiled Resource:
------------------
# Declared in /opt/scalr-server/embedded/cookbooks/scalr-server/recipes/group_service_always_post.rb:5:in `block in from_file'
supervisor_service("service-analytics_poller") do
action [:enable, :start]
updated true
retries 0
retry_delay 2
default_guard_interpreter :default
declared_type :supervisor_service
cookbook_name :"scalr-server"
recipe_name "group_service_always_post"
command "/opt/scalr-server/libexec/service/scalrpy_proxy /opt/scalr-server/var/run/service/analytics_poller.pid /opt/scalr-server/embedded/bin/python /opt/scalr-server/embedded/scalr/app/python/scalrpy/analytics_poller.py --pid-file=/opt/scalr-server/var/run/service/analytics_poller.pid --log-file=/opt/scalr-server/var/log/service/python-analytics_poller.log --user=scalr-app --group=scalr-app --config=/opt/scalr-server/embedded/scalr/app/etc/config.yml --verbosity=INFO "
stdout_logfile "/opt/scalr-server/var/log/supervisor/service-analytics_poller.log"
stderr_logfile "/opt/scalr-server/var/log/supervisor/service-analytics_poller.err"
autostart true
startsecs 1
service_name "service-analytics_poller"
process_name "%(program_name)s"
numprocs 1
numprocs_start 0
priority 999
autorestart :unexpected
startretries 3
exitcodes [0, 2]
stopsignal :TERM
stopwaitsecs 10
stdout_logfile_maxbytes "50MB"
stdout_logfile_backups 10
stdout_capture_maxbytes "0"
stderr_logfile_maxbytes "50MB"
stderr_logfile_backups 10
stderr_capture_maxbytes "0"
serverurl "AUTO"
end
Running handlers:
[2016-11-30T09:37:25-05:00] ERROR: Running exception handlers
- Raven::Chef::SentryHandler
Running handlers complete
[2016-11-30T09:37:26-05:00] ERROR: Exception handlers complete
[2016-11-30T09:37:26-05:00] FATAL: Stacktrace dumped to /opt/scalr-server/embedded/cookbooks/cache/chef-stacktrace.out
Chef Client failed. 53 resources updated in 10.841172558 seconds
[2016-11-30T09:37:26-05:00] ERROR: supervisor_service[service-analytics_poller] (scalr-server::group_service_always_post line 5) had an error: RuntimeError: Supervisor service service-analytics_poller was unable to be started
[2016-11-30T09:37:26-05:00] FATAL: Chef::Exceptions::ChildConvergeError: Chef run process exited unsuccessfully (exit code 1)
I want to use the f command (to go to next occurence of a character) in a python file but somehow this is masked by code folding function.
:set nofoldenable doesn't work.
These options are in my .vimrc:
filetype off
filetype plugin indent on
syntax on
Does someone know which plug-in causes this behavior and how I can toggle between the two functionalities?
Here is the output of :scriptnames
1: ~/.vimrc
2: /usr/local/share/vim/vim74/ftoff.vim
3: /usr/local/share/vim/vim74/filetype.vim
4: /usr/local/share/vim/vim74/ftplugin.vim
5: /usr/local/share/vim/vim74/indent.vim
6: /usr/local/share/vim/vim74/syntax/syntax.vim
7: /usr/local/share/vim/vim74/syntax/synload.vim
8: /usr/local/share/vim/vim74/syntax/syncolor.vim
9: ~/.vim/autoload/pathogen.vim
10: ~/.vim/bundle/SWTC.vim/plugin/SWTC.vim
11: ~/.vim/bundle/SWTC.vim/plugin/rng.vim
12: ~/.vim/bundle/jedi-vim/plugin/jedi.vim
13: ~/.vim/bundle/jedi-vim/autoload/jedi.vim
14: ~/.vim/bundle/syntastic/plugin/syntastic/autoloclist.vim
15: ~/.vim/bundle/syntastic/plugin/syntastic/balloons.vim
16: ~/.vim/bundle/syntastic/plugin/syntastic/checker.vim
17: ~/.vim/bundle/syntastic/plugin/syntastic/cursor.vim
18: ~/.vim/bundle/syntastic/plugin/syntastic/highlighting.vim
19: ~/.vim/bundle/syntastic/plugin/syntastic/loclist.vim
20: ~/.vim/bundle/syntastic/plugin/syntastic/modemap.vim
21: ~/.vim/bundle/syntastic/plugin/syntastic/notifiers.vim
22: ~/.vim/bundle/syntastic/plugin/syntastic/registry.vim
23: ~/.vim/bundle/syntastic/plugin/syntastic/signs.vim
24: ~/.vim/bundle/syntastic/plugin/syntastic.vim
25: ~/.vim/bundle/syntastic/autoload/syntastic/util.vim
26: ~/.vim/bundle/vim-show-whitespace/plugin/showwhite.vim
27: ~/.vim/bundle/vim-surround/plugin/surround.vim
28: /usr/local/share/vim/vim74/plugin/getscriptPlugin.vim
29: /usr/local/share/vim/vim74/plugin/gzip.vim
30: /usr/local/share/vim/vim74/plugin/matchparen.vim
31: /usr/local/share/vim/vim74/plugin/netrwPlugin.vim
Run the map f command to see if there's a mapping for the f key.
If there is such a mapping, you can see which configuration file mapped the key by running verbose map f. It should report something like:
Last set from ~/.vim/some-plugin.vim