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Sasha G

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Apr 25, 2022, 1:23:18 PM4/25/22
to majiq_voila
Hello, 

I just have a few questions on using viola. So first I downloaded gunicorn for the web server. I am not sure what the order of commands is next. I did the following. 

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 '



Paul Jewell

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Apr 27, 2022, 9:55:11 AM4/27/22
to majiq_voila
Hi Sasha,

Some versions of Mac OSX have had some issue with python3.8's multiprocessing library. Can you please try to add the switch "-j 1" to your command to disable multiprocessing? Something like:

$ voila view -j 1 -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

Apologies for the interruption, let me know if this helps or provides a different error.

Wojciech Teodorowicz

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Jul 14, 2022, 10:47:31 AM7/14/22
to majiq_voila
Hi Paul, 

- j 1 function does not help for voila modulize


$(magic) Hamrek-iMac-Three:Desktop labuser$ 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 10:45:01,222 (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 '



Paul Jewell

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Jul 27, 2022, 11:16:10 AM7/27/22
to majiq_voila
Hi Hamrek,

Can you please try one more switch? Instead of -j 1 can you try --debug? This should disable even loading the multiprocessing library.

Thanks.
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