When I install pyguppyclient to connect Guppy, Errors occurred.
(venv3)software/pyguppyclient$ make test
mkdir -p tests/reads
wget -q --show-progress --max-redirect=9 -O tests/reads/reads.tar.gz https://nan oporetech.box.com/shared/static/hpeyme4posfzmc0hcxh0nl5tiuzjfbzf.gz
tests/reads/reads.t 100%[===================>] 15.45M 96.9KB/s in 2m 42s
tar xf tests/reads/reads.tar.gz -C tests/reads
rm tests/reads/reads.tar.gz
nosetests -v --with-doctest --with-coverage --cover-package pyguppyclient
Doctest: pyguppyclient.utils.bases_fmt ... ok
Doctest: pyguppyclient.utils.batches ... ok
Doctest: pyguppyclient.utils.distribute ... ok
Doctest: pyguppyclient.utils.parse_config ... ok
test the caller ... ERROR
test loaded configs ... ERROR
try and load in invalid config ... ERROR
test a read with state ... ERROR
test a read without state ... ERROR
test the client api without sending a read ... ERROR
======================================================================
ERROR: test the caller
----------------------------------------------------------------------
concurrent.futures.process._RemoteTraceback:
"""
Traceback (most recent call last):
File "/media/mdb2/disk4/anaconda3/lib/python3.7/concurrent/futures/process.py" , line 239, in _process_worker
r = call_item.fn(*call_item.args, **call_item.kwargs)
File "/media/mdb2/disk4/anaconda3/lib/python3.7/concurrent/futures/process.py" , line 198, in _process_chunk
return [fn(*args) for args in chunk]
File "/media/mdb2/disk4/anaconda3/lib/python3.7/concurrent/futures/process.py" , line 198, in <listcomp>
return [fn(*args) for args in chunk]
File "/media/mdb2/disk3/haoy/software/pyguppyclient/pyguppyclient/caller.py", line 74, in basecall_batch
with GuppyBasecallerClient(config_name=self.config, host=self.host, port=sel f.port) as client:
File "/media/mdb2/disk3/haoy/software/pyguppyclient/pyguppyclient/client.py", line 43, in __enter__
self.connect()
File "/media/mdb2/disk3/haoy/software/pyguppyclient/pyguppyclient/client.py", line 81, in connect
self.pcl_client.get_error_message())
ConnectionError: Connect with 'dna_r9.4.1_450bps_fast' failed: Could not get det ails from server (invalid response).
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/media/mdb2/disk3/haoy/software/pyguppyclient/tests/caller_tests.py", li ne 19, in test_caller
caller.basecall(self.files)
File "/media/mdb2/disk3/haoy/software/pyguppyclient/pyguppyclient/caller.py", line 61, in basecall
return sum(pool.map(self.basecall_batch, work))
File "/media/mdb2/disk4/anaconda3/lib/python3.7/concurrent/futures/process.py" , line 483, in _chain_from_iterable_of_lists
for element in iterable:
File "/media/mdb2/disk4/anaconda3/lib/python3.7/concurrent/futures/_base.py", line 598, in result_iterator
yield fs.pop().result()
File "/media/mdb2/disk4/anaconda3/lib/python3.7/concurrent/futures/_base.py", line 435, in result
return self.__get_result()
File "/media/mdb2/disk4/anaconda3/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
ConnectionError: Connect with 'dna_r9.4.1_450bps_fast' failed: Could not get det ails from server (invalid response).
======================================================================
ERROR: test loaded configs
----------------------------------------------------------------------
Traceback (most recent call last):
File "/media/mdb2/disk3/haoy/software/pyguppyclient/tests/client_tests.py", li ne 20, in setUp
self.client.connect()
File "/media/mdb2/disk3/haoy/software/pyguppyclient/pyguppyclient/client.py", line 81, in connect
self.pcl_client.get_error_message())
ConnectionError: Connect with 'dna_r9.4.1_450bps_fast' failed: Could not get det ails from server (invalid response).
======================================================================
ERROR: try and load in invalid config
----------------------------------------------------------------------
Traceback (most recent call last):
File "/media/mdb2/disk3/haoy/software/pyguppyclient/tests/client_tests.py", li ne 20, in setUp
self.client.connect()
File "/media/mdb2/disk3/haoy/software/pyguppyclient/pyguppyclient/client.py", line 81, in connect
self.pcl_client.get_error_message())
ConnectionError: Connect with 'dna_r9.4.1_450bps_fast' failed: Could not get det ails from server (invalid response).
======================================================================
ERROR: test a read with state
----------------------------------------------------------------------
Traceback (most recent call last):
File "/media/mdb2/disk3/haoy/software/pyguppyclient/tests/client_tests.py", li ne 20, in setUp
self.client.connect()
File "/media/mdb2/disk3/haoy/software/pyguppyclient/pyguppyclient/client.py", line 81, in connect
self.pcl_client.get_error_message())
ConnectionError: Connect with 'dna_r9.4.1_450bps_fast' failed: Could not get det ails from server (invalid response).
======================================================================
ERROR: test a read without state
----------------------------------------------------------------------
Traceback (most recent call last):
File "/media/mdb2/disk3/haoy/software/pyguppyclient/tests/client_tests.py", li ne 20, in setUp
self.client.connect()
File "/media/mdb2/disk3/haoy/software/pyguppyclient/pyguppyclient/client.py", line 81, in connect
self.pcl_client.get_error_message())
ConnectionError: Connect with 'dna_r9.4.1_450bps_fast' failed: Could not get det ails from server (invalid response).
======================================================================
ERROR: test the client api without sending a read
----------------------------------------------------------------------
Traceback (most recent call last):
File "/media/mdb2/disk3/haoy/software/pyguppyclient/tests/client_tests.py", li ne 20, in setUp
self.client.connect()
File "/media/mdb2/disk3/haoy/software/pyguppyclient/pyguppyclient/client.py", line 81, in connect
self.pcl_client.get_error_message())
ConnectionError: Connect with 'dna_r9.4.1_450bps_fast' failed: Could not get det ails from server (invalid response).
Name Stmts Miss Cover Mis sing
-------------------------------------------------------------------------------- ----
pyguppyclient/__init__.py 7 0 100%
pyguppyclient/caller.py 47 17 64% 70- 94
pyguppyclient/client.py 147 83 44% 43- 44, 47, 50-59, 62-70, 77, 85, 88, 91-92, 95, 98-105, 124-133, 141-149, 158-167, 170-171, 174, 177-189, 192-197, 204, 207-208, 211-212, 215-222, 228-236, 245
pyguppyclient/decode.py 107 85 21% 25- 28, 44-51, 83-101, 107-109, 112-120, 127-216, 226-227
pyguppyclient/guppy_ipc/AlignmentIndex.py 29 14 52% 14- 17, 21, 25, 29-32, 36-39
pyguppyclient/guppy_ipc/AlignmentResults.py 125 78 38% 14- 17, 21, 25, 29-32, 36-39, 43-46, 50-53, 57-60, 64-67, 71-74, 78-81, 85-88, 92-95 , 99-102, 106-109, 113-116, 120-123, 127-130, 134-137, 141-144, 148-151
pyguppyclient/guppy_ipc/BarcodeArrangementResults.py 123 82 33% 14- 17, 21, 25, 29-32, 36-39, 43-46, 50-53, 57-60, 64-67, 71-74, 78-85, 89-96, 100-1 07, 111-118, 122-125, 129-132, 136-139, 143-146
pyguppyclient/guppy_ipc/BarcodeKitDefinition.py 71 42 41% 14- 17, 21, 25, 29-32, 36-39, 43-46, 50-53, 57-60, 64-67, 71-74, 78-81, 85-88
pyguppyclient/guppy_ipc/BarcodeMidDetectResults.py 35 18 49% 14- 17, 21, 25, 29-32, 36-39, 43-46
pyguppyclient/guppy_ipc/BarcodeResults.py 47 26 45% 14- 17, 21, 25, 29-32, 36-39, 43-46, 50-53, 57-60
pyguppyclient/guppy_ipc/BaseModData.py 50 29 42% 14- 17, 21, 25, 29-32, 36-39, 43-47, 51-54, 58-61, 65-66
pyguppyclient/guppy_ipc/CalledBlockData.py 206 140 32% 14- 17, 21, 25, 29-32, 36-39, 43-46, 50-53, 57-60, 64-67, 71-74, 78-81, 85-88, 92-95 , 99-102, 106-109, 113-116, 120-123, 127-130, 134-137, 141-144, 148-155, 159-162 , 166-172, 176-183, 187-191, 195-198, 202-205, 209-210, 214-221, 225-234, 238-24 1, 245-246
pyguppyclient/guppy_ipc/ClientStats.py 29 14 52% 14- 17, 21, 25, 29-32, 36-39
pyguppyclient/guppy_ipc/ConfigData.py 96 65 32% 14- 17, 21, 25, 29-38, 42-45, 49-50, 54-63, 67-70, 74-75, 79-83, 87-90, 94-95, 99-10 8, 112-115, 119-120
pyguppyclient/guppy_ipc/Configuration.py 65 38 42% 14- 17, 21, 25, 29-32, 36-39, 43-46, 50-53, 57-60, 64-67, 71-74, 78-81
pyguppyclient/guppy_ipc/Content.py 7 0 100%
pyguppyclient/guppy_ipc/FlipflopTraceData.py 59 36 39% 14- 17, 21, 25, 29-33, 37-40, 44-47, 51-52, 56-60, 64-67, 71-74, 78-79
pyguppyclient/guppy_ipc/MessageData.py 48 29 40% 14- 17, 21, 25, 29-36, 40-43, 47-50, 54-60
pyguppyclient/guppy_ipc/ProtocolVersion.py 16 6 62% 14, 24-28
pyguppyclient/guppy_ipc/ReadBlockData.py 106 69 35% 14- 17, 21, 25, 29-32, 36-39, 43-46, 50-53, 57-60, 64-67, 71-74, 78-81, 85-89, 93-96 , 100-103, 107-108, 112-119, 123-130
pyguppyclient/guppy_ipc/ReadBlockType.py 5 0 100%
pyguppyclient/guppy_ipc/RunlengthTraceData.py 149 100 33% 14- 17, 21, 25, 29-32, 36-40, 44-47, 51-54, 58-59, 63-67, 71-74, 78-81, 85-86, 90-94 , 98-101, 105-108, 112-113, 117-121, 125-128, 132-135, 139-140, 144-148, 152-155 , 159-162, 166-167, 171-175, 179-182, 186-189, 193-194
pyguppyclient/guppy_ipc/ScalingData.py 53 30 43% 14- 17, 21, 25, 29-32, 36-39, 43-46, 50-53, 57-60, 64-67
pyguppyclient/guppy_ipc/ScalingOverrideData.py 29 14 52% 14- 17, 21, 25, 29-32, 36-39
pyguppyclient/guppy_ipc/ServerStats.py 62 38 39% 14- 17, 21, 25, 29-32, 36-39, 43-46, 50-53, 57-66, 70-73, 77-78
pyguppyclient/guppy_ipc/SimpleReplyData.py 35 18 49% 14- 17, 21, 25, 29-32, 36-39, 43-46
pyguppyclient/guppy_ipc/SimpleReplyType.py 17 0 100%
pyguppyclient/guppy_ipc/SimpleRequestData.py 35 18 49% 14- 17, 21, 25, 29-32, 36-39, 43-46
pyguppyclient/guppy_ipc/SimpleRequestType.py 14 0 100%
pyguppyclient/guppy_ipc/TraceData.py 4 0 100%
pyguppyclient/guppy_ipc/__init__.py 0 0 100%
pyguppyclient/io.py 24 14 42% 17- 23, 32, 39-40, 47-50
pyguppyclient/ipc.py 69 50 28% 31- 86, 90-143
pyguppyclient/utils.py 24 0 100%
-------------------------------------------------------------------------------- ----
TOTAL 1940 1153 41%
----------------------------------------------------------------------
Ran 10 tests in 0.530s
FAILED (errors=6)
make: *** [Makefile:21: test] Error 1
When I install pyguppyclient to connect Guppy, Errors occurred.
system: Ubuntu16.04
python: 3.7.4.
Guppy: v4.2.2 or v4.4.1, I've tried 2 versions
pyguppyclent: v0.0.6 or v0.07a
any advice to solve the problem?
Thanks