I'm having the following error when trying to run rmats2sashimiplot:
Reading sample label: Abi3bp Controls-1 IncLevel: 0.89
Error retrieving files from chr16: invalid reference chr16
Are you sure chr16 appears in your BAM file?
Aborting plot...
Traceback (most recent call last):
File "/data/home/bt21020/.conda/envs/py.2.7/lib/python2.7/site-packages/MISO/misopy/sa
shimi_plot/sashimi_plot.py", line 293, in
main()
File "/data/home/bt21020/.conda/envs/py.2.7/lib/python2.7/site-packages/MISO/misopy/sa
shimi_plot/sashimi_plot.py", line 289, in main
plot_label=plot_label)
File "/data/home/bt21020/.conda/envs/py.2.7/lib/python2.7/site-packages/MISO/misopy/sa
shimi_plot/sashimi_plot.py", line 160, in plot_event
plot_label=plot_label)
File "/data/home/bt21020/.conda/envs/py.2.7/lib/python2.7/site-packages/MISO/misopy/sa
shimi_plot/plot_utils/plot_gene.py", line 838, in plot_density_from_file
plot_title=plot_title)
File "/data/home/bt21020/.conda/envs/py.2.7/lib/python2.7/site-packages/MISO/misopy/sa
shimi_plot/plot_utils/plot_gene.py", line 392, in plot_density
junction_log_base=junction_log_base)
TypeError: 'AxesSubplot' object is not iterable
mv: cannot stat ‘/data/scratch/bt21020/2022-05-16-sashimi/result/HGS2/test/Sashimi_plot/
chr16:56592604:56592681:+#chr16:56594462:56594536:+#chr16:56642489:56642560:+.pdf’: No s
uch file or directory
I'm using bam files from rmats output so does this mean I have to edit the bam files for the chr column? Please help thank you.
Related
did anyone know why this error happen? other solver such as cbc works fine but when sent to NEOS, I got the following error in command line
Traceback (most recent call last):
File "C:\repos\work_packager\Test\Scratch\Networkx_Sample\testss.py", line 409, in
process_data(df, df)
File "C:\repos\work_packager\Test\Scratch\Networkx_Sample\testss.py", line 191, in process_data
pyomo_tool(df,road_year, pit_year, road_estimated_cost, pit_estimated_cost, road_tot_budget, pit_tot_budget,
File "C:\repos\work_packager\Test\Scratch\Networkx_Sample\testss.py", line 291, in pyomo_tool
solver.solve(model)
File "C:\Python31\lib\site-packages\pyomo\opt\results\container.py", line 284, in getattr
raise AttributeError("Unknown attribute "+str(name)+"' for object with type "+str(type(self))) AttributeError: Unknown attribute solve' for object with type <class 'pyomo.opt.results.results_.SolverResults'>
I am trying to run the SONOS self test for a music service on Sonos.
After getting the dependencies, and filling out the config file, I try to run the python Sonos selftest, however it runs into an error and I have no clue what the underlying issue might be to get it running:
No handlers could be found for logger "smapi"
Traceback (most recent call last):
File "suite_selftest.py", line 226, in <module>
nightly_mode(parser.config_file)
File "suite_selftest.py", line 51, in nightly_mode
development_mode(config_file)
File "suite_selftest.py", line 186, in development_mode
fixtures.append(getlastupdate.PollingIntervalTest(suite.client, suite.smapiservice))
File "/Users/thomas/Desktop/PythonSelfTest/smapi/content_workflow/getlastupdate.py", line 20, in __init__
self.poll_interval = self.smapiservice.get_polling_interval()
File "../../sonos-1.1.0.dev_r300235-py2.7.egg/sonos/smapi/smapiservice.py", line 465, in get_polling_interval
File "/usr/local/Cellar/python#2/2.7.15_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/ConfigParser.py", line 362, in getfloat
return self._get(section, float, option)
File "/usr/local/Cellar/python#2/2.7.15_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/ConfigParser.py", line 356, in _get
return conv(self.get(section, option))
ValueError: could not convert string to float:
Found the fix already, forgot to add the Polling Interval in the config file...
I hope somebody here can help. I've been googling this error like crazy but haven't found anything.
I have a pipeline that works perfectly when executed locally but it fails when executed on GCP. The following are the error messages that I get.
Workflow failed. Causes: S03:Write transform
fn/WriteMetadata/ResolveBeamFutures/CreateSingleton/Read+Write
transform fn/WriteMetadata/ResolveBeamFutures/ResolveFutures/Do+Write
transform fn/WriteMetadata/WriteMetadata failed., A work item was
attempted 4 times without success. Each time the worker eventually
lost contact with the service. The work item was attempted on:
Traceback (most recent call last): File "preprocess.py", line 491,
in
main() File "preprocess.py", line 487, in main
transform_data(args,pipeline_options,runner) File "preprocess.py", line 451, in transform_data
eval_data |= 'Identity eval' >> beam.ParDo(Identity()) File "/Library/Python/2.7/site-packages/apache_beam/pipeline.py", line 335,
in exit
self.run().wait_until_finish() File "/Library/Python/2.7/site-packages/apache_beam/runners/dataflow/dataflow_runner.py",
line 897, in wait_until_finish
(self.state, getattr(self._runner, 'last_error_msg', None)), self) apache_beam.runners.dataflow.dataflow_runner.DataflowRuntimeException:
Dataflow pipeline failed. State: FAILED, Error: Traceback (most recent
call last): File
"/usr/local/lib/python2.7/dist-packages/dataflow_worker/batchworker.py",
line 582, in do_work
work_executor.execute() File "/usr/local/lib/python2.7/dist-packages/dataflow_worker/executor.py",
line 166, in execute
op.start() File "apache_beam/runners/worker/operations.py", line 294, in apache_beam.runners.worker.operations.DoOperation.start
(apache_beam/runners/worker/operations.c:10607)
def start(self): File "apache_beam/runners/worker/operations.py", line 295, in
apache_beam.runners.worker.operations.DoOperation.start
(apache_beam/runners/worker/operations.c:10501)
with self.scoped_start_state: File "apache_beam/runners/worker/operations.py", line 300, in
apache_beam.runners.worker.operations.DoOperation.start
(apache_beam/runners/worker/operations.c:9702)
pickler.loads(self.spec.serialized_fn)) File "/usr/local/lib/python2.7/dist-packages/apache_beam/internal/pickler.py",
line 225, in loads
return dill.loads(s) File "/usr/local/lib/python2.7/dist-packages/dill/dill.py", line 277, in
loads
return load(file) File "/usr/local/lib/python2.7/dist-packages/dill/dill.py", line 266, in
load
obj = pik.load() File "/usr/lib/python2.7/pickle.py", line 858, in load
dispatchkey File "/usr/lib/python2.7/pickle.py", line 1083, in load_newobj
obj = cls.new(cls, *args) TypeError: new() takes exactly 4 arguments (1 given)
Any ideas??
Thanks,
Pedro
If the pipeline works locally but fails on GCP it's possible that you're running into a version mismatch.
What TF, tf.Transform, beam versions are you running locally and on GCP?
Trying to build an executable file using pyinstaller. I keep getting the below error
Traceback (most recent call last):
File "Inventory_Computation\app.py", line 145, in <module>
File "flask\app.py", line 843, in run
File "werkzeug\serving.py", line 692, in run_simple
File "werkzeug\_reloader.py", line 248, in run_with_reloader
File "werkzeug\_reloader.py", line 129, in run
File "werkzeug\_reloader.py", line 22, in _iter_module_files
File "Lib\email\__init__.py", line 79, in __getattr__
ImportError: No module named message
Failed to execute script app
found the solution finally...
Go to "C:\Python27\Lib\email"
And find the "init.py"
Comment out below lines.
'Audio',
'Base',
'Image',
'Message',
'Multipart',
'NonMultipart',
'Text',
Try pyinstaller again
I have installed package envoy. I ran the script but a windows error occured .I commented envoy.run then the full script runs but when I remove the comment, error occurs.
import envoy
# This data is checked-in to the repository and is a compressed
# version of the output from Example 3
F = 'resources/ch06-mailboxes/data/enron.mbox.json.bz2'
r = envoy.run("bunzip2 %s" % (F,))
print r.std_out
print r.std_err
traceback of script:
Exception in thread Thread-9:
Traceback (most recent call last):
File "C:\Users\sachin\Anaconda\lib\threading.py", line 810, in __bootstrap_inner
self.run()
File "C:\Users\sachin\Anaconda\lib\threading.py", line 763, in run
self.__target(*self.__args, **self.__kwargs)
File "C:\Users\sachin\Anaconda\lib\site-packages\envoy\core.py", line 40, in target
bufsize=0,
File "C:\Users\sachin\Anaconda\lib\subprocess.py", line 709, in __init__
errread, errwrite)
File "C:\Users\sachin\Anaconda\lib\subprocess.py", line 957, in _execute_child
startupinfo)
WindowsError: [Error 2] The system cannot find the file specified
Please try this:
F = os.path.join(os.getcwd(), 'resources/ch06-mailboxes/data/enron.mbox.json.bz2')