2022-04-25 13:17:37,112 (PID:28815) - INFO - Command: /Users/sasha/majiq_env/bin/voila view -p 8000 --host 127.0.0.1 /Users/sasha/Downloads/Splicegraph_and_majiq_files/deltapsi/Group_1-Group_2.deltapsi.voila
2022-04-25 13:17:37,112 (PID:28815) - INFO - Voila v2.4.dev3+g85d07819
2022-04-25 13:17:37,112 (PID:28815) - INFO - config file: /var/folders/_6/w95_jy1x1n14fq8fjx7cnncc0000gn/T/tmpbd25kg1i
2022-04-25 13:17:37,147 (PID:28815) - ERROR - Splice Graph file was not found.
(majiq_env) Sashas-MacBook-Pro-2:~ sasha$ voila view -p 8000 --host 127.0.0.1 /Users/sasha/Downloads/Splicegraph_and_majiq_files/build/splicegraph.sql
2022-04-25 13:20:37,378 (PID:28856) - INFO - Command: /Users/sasha/majiq_env/bin/voila view -p 8000 --host 127.0.0.1 /Users/sasha/Downloads/Splicegraph_and_majiq_files/build/splicegraph.sql
2022-04-25 13:20:37,378 (PID:28856) - INFO - Voila v2.4.dev3+g85d07819
2022-04-25 13:20:37,378 (PID:28856) - INFO - config file: /var/folders/_6/w95_jy1x1n14fq8fjx7cnncc0000gn/T/tmpu8jmbit1
2022-04-25 13:20:37,429 (PID:28856) - ERROR - No Voila files were found in the files or directories provided.
(majiq_env) Sashas-MacBook-Pro-2:~ sasha$ voila view -p 8000 --host 127.0.0.1 /Users/sasha/Downloads/Splicegraph_and_majiq_files/build/splicegraph.sql /Users/sasha/Downloads/Splicegraph_and_majiq_files/deltapsi/Group_1-Group_2.deltapsi.voila
2022-04-25 13:21:04,967 (PID:28865) - INFO - Command: /Users/sasha/majiq_env/bin/voila view -p 8000 --host 127.0.0.1 /Users/sasha/Downloads/Splicegraph_and_majiq_files/build/splicegraph.sql /Users/sasha/Downloads/Splicegraph_and_majiq_files/deltapsi/Group_1-Group_2.deltapsi.voila
2022-04-25 13:21:04,967 (PID:28865) - INFO - Voila v2.4.dev3+g85d07819
2022-04-25 13:21:04,967 (PID:28865) - INFO - config file: /var/folders/_6/w95_jy1x1n14fq8fjx7cnncc0000gn/T/tmpk321hz7y
2022-04-25 13:21:05,033 (PID:28865) - INFO - Creating index: /Users/sasha/Downloads/Splicegraph_and_majiq_files/deltapsi/Group_1-Group_2.deltapsi.voila
Indexing LSV IDs: 0 / 39752
Indexing LSV IDs: 0 / 39752
2022-04-25 13:21:20,717 (PID:28865) - INFO - Writing index: /Users/sasha/Downloads/Splicegraph_and_majiq_files/deltapsi/Group_1-Group_2.deltapsi.voila
2022-04-25 13:21:20,717 (PID:28865) - ERROR - 'FILES'
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 48, in mapstar
return list(map(*args))
File "/Users/sasha/majiq_env/lib/python3.9/site-packages/rna_voila/index.py", line 242, in _deltapsi_pool_add_index
with ViewDeltaPsi() as m:
File "/Users/sasha/majiq_env/lib/python3.9/site-packages/rna_voila/api/view_matrix.py", line 456, in __init__
self.config = ViewConfig()
File "/Users/sasha/majiq_env/lib/python3.9/site-packages/rna_voila/config.py", line 304, in __new__
'voila_files': config_parser['FILES']['voila'].split('\n'),
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/configparser.py", line 960, in __getitem__
raise KeyError(key)
KeyError: 'FILES'
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/Users/sasha/majiq_env/lib/python3.9/site-packages/rna_voila/run_voila.py", line 438, in main
args.func()
File "/Users/sasha/majiq_env/lib/python3.9/site-packages/rna_voila/view/views.py", line 79, in run_service
run_app = get_app()
File "/Users/sasha/majiq_env/lib/python3.9/site-packages/rna_voila/view/views.py", line 105, in get_app
Index()
File "/Users/sasha/majiq_env/lib/python3.9/site-packages/rna_voila/index.py", line 49, in __init__
index()
File "/Users/sasha/majiq_env/lib/python3.9/site-packages/rna_voila/index.py", line 316, in _deltapsi
voila_index = voila_index.get()
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 771, in get
raise self._value
KeyError: 'FILES'
Exception ignored in: <function Pool.__del__ at 0x7fdca8c5c0d0>
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 268, in __del__
self._change_notifier.put(None)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/queues.py", line 378, in put
self._writer.send_bytes(obj)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py", line 205, in send_bytes
self._send_bytes(m[offset:offset + size])
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py", line 416, in _send_bytes
self._send(header + buf)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py", line 373, in _send
n = write(self._handle, buf)
OSError: [Errno 9] Bad file descriptor
(majiq_env) Sashas-MacBook-Pro-2:~ sasha$ /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/resource_tracker.py:216: UserWarning: resource_tracker: There appear to be 3 leaked semaphore objects to clean up at shutdown
warnings.warn('resource_tracker: There appear to be %d '
2022-07-14 10:45:01,222 (PID:89057) - INFO - Command: /Users/labuser/opt/anaconda3/envs/magic/bin/voila modulize -d /Users/labuser/Desktop/NOVOGENE-N/output_majiq_without_outlier/voila /Users/labuser/Desktop/NOVOGENE-N/output_majiq_without_outlier/build/splicegraph.sql /Users/labuser/Desktop/NOVOGENE-N/output_majiq_without_outlier/deltapsi -j 1
2022-07-14 10:45:01,223 (PID:89057) - INFO - Voila v2.4.dev3+g85d07819
2022-07-14 10:45:01,223 (PID:89057) - INFO - config file: /var/folders/jt/sjrqs3ws2n7gv835w38h9dy00000gp/T/tmpj4k1116y
2022-07-14 10:45:01,250 (PID:89057) - INFO - dPSIx1 MODULIZE
2022-07-14 10:45:02,149 (PID:89057) - INFO - Modulizing 61498 gene(s)
2022-07-14 10:45:02,149 (PID:89057) - INFO - Quantifications based on 1 input file(s)
2022-07-14 10:45:02,150 (PID:89057) - INFO - ╔═══════════════════════════════════════════════════════════════╗
2022-07-14 10:45:02,150 (PID:89057) - INFO - ╠╡ Before Modulization: ║
2022-07-14 10:45:02,150 (PID:89057) - INFO - ║ Dropping junctions with max(PSI) < 0.050 ║
2022-07-14 10:45:02,150 (PID:89057) - INFO - ║ Dropping junctions with max(number_of_reads) < 1 ║
2022-07-14 10:45:02,150 (PID:89057) - INFO - ╠╡ After Modulization: ║
2022-07-14 10:45:02,150 (PID:89057) - INFO - ║ Dropping modules if none(max(E(|dPSI|)) >= 0.200) ║
2022-07-14 10:45:02,150 (PID:89057) - INFO - ║ Dropping modules if none(max(P(|dPSI|>=0.200)) >= 0.950) ║
2022-07-14 10:45:02,150 (PID:89057) - INFO - ╚═══════════════════════════════════════════════════════════════╝
2022-07-14 10:45:02,150 (PID:89057) - INFO - Writing TSVs to /Users/labuser/Desktop/NOVOGENE-N/output_majiq_without_outlier/voila
2022-07-14 10:45:04,811 (PID:89057) - ERROR - 'FILES'
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/Users/labuser/opt/anaconda3/envs/magic/lib/python3.8/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/Users/labuser/opt/anaconda3/envs/magic/lib/python3.8/multiprocessing/pool.py", line 48, in mapstar
return list(map(*args))
File "/Users/labuser/opt/anaconda3/envs/magic/lib/python3.8/site-packages/rna_voila/classify.py", line 75, in classify_gene
config = ClassifyConfig()
File "/Users/labuser/opt/anaconda3/envs/magic/lib/python3.8/site-packages/rna_voila/config.py", line 381, in __new__
'voila_files': config_parser['FILES']['voila'].split('\n'),
File "/Users/labuser/opt/anaconda3/envs/magic/lib/python3.8/configparser.py", line 960, in __getitem__
raise KeyError(key)
KeyError: 'FILES'
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/Users/labuser/opt/anaconda3/envs/magic/lib/python3.8/site-packages/rna_voila/run_voila.py", line 438, in main
args.func()
File "/Users/labuser/opt/anaconda3/envs/magic/lib/python3.8/site-packages/rna_voila/classify.py", line 37, in __init__
run_classifier()
File "/Users/labuser/opt/anaconda3/envs/magic/lib/python3.8/site-packages/rna_voila/classify.py", line 236, in run_classifier
res = classifier_pool.get()
File "/Users/labuser/opt/anaconda3/envs/magic/lib/python3.8/multiprocessing/pool.py", line 771, in get
raise self._value
KeyError: 'FILES'
(magic) Hamrek-iMac-Three:Desktop labuser$ /Users/labuser/opt/anaconda3/envs/magic/lib/python3.8/multiprocessing/resource_tracker.py:216: UserWarning: resource_tracker: There appear to be 2 leaked semaphore objects to clean up at shutdown
warnings.warn('resource_tracker: There appear to be %d '