Stuck on an issue?

Lightrun Answers was designed to reduce the constant googling that comes with debugging 3rd party libraries. It collects links to all the places you might be looking at while hunting down a tough bug.

And, if you’re still stuck at the end, we’re happy to hop on a call to see how we can help out.

[Errno 28] No space left on device when importing SigProfilerExtractor

See original GitHub issue


I ran across this error when importing SigProfilerExtractor

>>> from SigProfilerExtractor import sigpro as sig /home/hannan/anaconda3/lib/python3.7/site-packages/joblib/ UserWarning: [Errno 28] No space left on device. joblib will operate in serial mode warnings.warn('%s. joblib will operate in serial mode' % (e,))

I checked both the memory and disk space and there is sufficient memory on both of them.

Screenshot from 2021-09-20 11-37-30

Here is the traceback when I tried to run the tool

Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/hannan/anaconda3/lib/python3.7/site-packages/SigProfilerExtractor/", line 823, in sigProfilerExtractor i = i) File "/home/hannan/anaconda3/lib/python3.7/site-packages/SigProfilerExtractor/", line 789, in decipher_signatures results = parallel_runs(excecution_parameters, genomes=genomes, totalProcesses=totalProcesses, verbose = False) File "/home/hannan/anaconda3/lib/python3.7/site-packages/SigProfilerExtractor/", line 685, in parallel_runs pool = multiprocessing.Pool() File "/home/hannan/anaconda3/lib/python3.7/multiprocessing/", line 119, in Pool context=self.get_context()) File "/home/hannan/anaconda3/lib/python3.7/multiprocessing/", line 158, in __init__ self._setup_queues() File "/home/hannan/anaconda3/lib/python3.7/multiprocessing/", line 251, in _setup_queues self._inqueue = self._ctx.SimpleQueue() File "/home/hannan/anaconda3/lib/python3.7/multiprocessing/", line 112, in SimpleQueue return SimpleQueue(ctx=self.get_context()) File "/home/hannan/anaconda3/lib/python3.7/multiprocessing/", line 332, in __init__ self._rlock = ctx.Lock() File "/home/hannan/anaconda3/lib/python3.7/multiprocessing/", line 67, in Lock return Lock(ctx=self.get_context()) File "/home/hannan/anaconda3/lib/python3.7/multiprocessing/", line 162, in __init__ SemLock.__init__(self, SEMAPHORE, 1, 1, ctx=ctx) File "/home/hannan/anaconda3/lib/python3.7/multiprocessing/", line 59, in __init__ unlink_now) OSError: [Errno 28] No space left on device

I was wondering if this error could be coming from the SigProfiler package or from the joblib/multiprocessing package? Any suggestions/insights would be much appreciated, thanks!

Warmest regards, Hannan

Issue Analytics

  • State:closed
  • Created 2 years ago
  • Comments:6

github_iconTop GitHub Comments

hannanwcommented, Sep 24, 2021

Hi Marcos,

Thanks! That suggestion worked, I am able to import and run SigProfilerExtractor now without issue.

Warmest regards, Hannan

marcos-diazgcommented, Sep 23, 2021

Hi again Hannan!

Please have a look at the first answer here. That should solve your issue since it seems that your /dev/shm is full. Hope that helps.

Best wishes,


Read more comments on GitHub >

github_iconTop Results From Across the Web

Python_OSError: [Errno 28] No space left on device
Late answer, but maybe usefull. I encountered a similar issue : OSError: [Errno 28] No space left on device: But, I have enough...
Read more >
SigProfilerExtractor Wiki - OSF
SigProfilerExtractor is a python framework that allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies ......
Read more >
The repertoire of mutational signatures in human cancer
signatures have also previously been described11,25,28–30. However, the ... and no primary cancers of this type were available.
Read more >
Errno 28 No space left on device even though there is space
... Failed to write server-info to /home/aswirbul/.local/share/jupyter/runtime/nbserver-71.json: [Errno 28] No space left on device.
Read more >
SigProfilerExtractor - PyPI
The tool identifies the number of operative mutational signatures, ... Next, open a python interpreter and import the SigProfilerExtractor module.
Read more >

github_iconTop Related Medium Post

No results found

github_iconTop Related StackOverflow Question

No results found

github_iconTroubleshoot Live Code

Lightrun enables developers to add logs, metrics and snapshots to live code - no restarts or redeploys required.
Start Free

github_iconTop Related Reddit Thread

No results found

github_iconTop Related Hackernoon Post

No results found

github_iconTop Related Tweet

No results found

github_iconTop Related Post

No results found

github_iconTop Related Hashnode Post

No results found