I have ran into this error and I am having trouble resolving it. Here is it what I get:
Traceback (most recent call last):
File "afile.py", line 100, in <module>
for col in bam.pileup( chrm, ps1, ps1+1,truncate=True):
File "pysam/calignmentfile.pyx", line 2060, in pysam.calignmentfile.IteratorColumnRegion.__next__
(pysam/calignmentfile.c:23305)
ValueError: error during iteration
Thanks a lot in advance.
i hit this recently. the root cause in my case was that the .bai bam index file was out of date. after i regenerated it with samtools index XXX.bam, the pysam crash went away.
Related
It gets stuck on the first urequests.get()
I have tried EVERYTHING, it prompts me this error
`Traceback (most recent call last):
File "<stdin>", line 26, in <module>
File "urequests.py", line 180, in get
File "urequests.py", line 76, in request
OSError: -1
`
Help please
Tried reinstalling the uf2, flash nuking it, importing manually urequests, NOTHING, i cant finish my prject without this.
today I asked this question concerning problems with PyTorch running on my GPU. In response, someone kindly suggested running the following code:
import os
num_gpus = os.environ['CUDA_VISIBLE_DEVICES'].split(',').__len__()
os.environ['CUDA_VISIBLE_DEVICES'] = ','.join(f'{i}' for i in range(num_gpus))
However, after running that second line, unfortunately I get another error:
num_gpus = os.environ['CUDA_VISIBLE_DEVICES'].split(',').__len__()
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/hbp/anaconda3/lib/python3.8/os.py", line 675, in __getitem__
raise KeyError(key) from None
KeyError: 'CUDA_VISIBLE_DEVICES'
I tried to look it up, but couldn't find anything helpful.
Does anyone have an idea what I could try? The question I linked to may have relevant info.
I am trying to run an audio to spectrogram script, namely:
https://github.com/grrrr/nsgt/tree/master/examples
When I try python spectrogram.py myaudio.wav
I get the error:
Traceback (most recent call last):
File "spectrogram.py", line 111, in <module>
coefs = assemble_coeffs(c, ncoefs)
File "spectrogram.py", line 27, in assemble_coeffs
out = np.empty((ncoefs,cq0.shape[1],cq0.shape[2]), dtype=cq0.dtype)
IndexError: tuple index out of range
Am I doing something wrong?
Please advise! :)
you can run it with just the argument --matrixform added.
I suggest you to see this issue! from the github project it can help you
What I get is this:
Traceback (most recent call last)
File "maian.py", line 24 in <module>
from web3 import web3
file "/usr/local/lib/python3.6/web3/__init__.py", line 5, in <module>
Correct me if I am wrong, but execution of program stops because the web3 thing (__init__.py) doesn't get loaded for some reason? How can I fix this?
What puzzles me again is that I'm not seeing a message at the very end telling me that something is wrong? I should now debug by trying to print some message...if it doesn't get printed then the program really stops while trying to initialize the web3 module?
Regarding this thread : http://goo.gl/uEyFua
I am experiencing a quite similar issue with the following code, trying to import a large Graph :
for (edge_id) in cursorSQL:
L.add((edge_id[2], str(edge_id[1])))
g = igraph.Graph.TupleList(L)
I get the following errors :
Traceback (most recent call last):
File "C.py", line 707, in __getitem__ return self._ids[item]
KeyError: '184840900'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
g = igraph.Graph.TupleList(L)
File "C:\Python34\lib\site-packages\igraph\__init__.py", line 2473, in TupleList
edge_list.append((idgen[item[0]], idgen[item[1]]))
File "C:\Python34\lib\site-packages\igraph\datatypes.py", line 709, in __getitem__
self._ids[item] = next(self._generator)
MemoryError
Just to make it clear. This code works perfectly until number of edges is too large (~4millions.)
Thanks.
Switched to python-64bits, and problem is now solved.
Problem was the 2GB-per-process limit in win7 for python-32bits.