"ValueError: Number of processes must be at least 1" in build

[Heewoong Lim]

Hi

I am trying Majiq 1.1.1

but get this error in build.

I also tried setting "-j" explicitly or "--disable-denovo" but got the same error.

Do you have any idea?

Thank you.

- Lim

majiq build -c build.conf -o output  ensembl.mm10.gff3
/mnt/data/heewlim/MLPT/RNAseq.mm10/Majiq/VirEnv/lib/python3.5/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
  from ._conv import register_converters as _register_converters
2018-05-01 18:02:20,812 (PID:4923) - INFO - Majiq Build v1.1.1
2018-05-01 18:02:20,813 (PID:4923) - INFO - Command: /mnt/data/heewlim/MLPT/RNAseq.mm10/Majiq/VirEnv/bin/majiq build -c build.conf -o output ensembl.mm10.gff3
2018-05-01 18:02:20,831 (PID:4923) - INFO - PRE DB 93.38 MB
2018-05-01 18:02:20,832 (PID:4923) - INFO - ... waiting gff3 parsing
2018-05-01 18:02:20,838 (PID:4938) - INFO - [Th 0]: START child,Process-2
2018-05-01 18:03:01,434 (PID:4923) - INFO - Retrieve denovo features
2018-05-01 18:03:01,434 (PID:4923) - INFO - Create 0 processes
Traceback (most recent call last):
  File "/mnt/data/heewlim/MLPT/RNAseq.mm10/Majiq/VirEnv/bin/majiq", line 9, in <module>
    load_entry_point('majiq==1.1.1', 'console_scripts', 'majiq')()
  File "/mnt/data/heewlim/MLPT/RNAseq.mm10/Majiq/VirEnv/lib/python3.5/site-packages/majiq/run_majiq.py", line 204, in main
    args.func(args)
  File "/mnt/data/heewlim/MLPT/RNAseq.mm10/Majiq/VirEnv/lib/python3.5/site-packages/majiq/src/build.py", line 32, in build
    pipeline_run(Builder(args))
  File "/mnt/data/heewlim/MLPT/RNAseq.mm10/Majiq/VirEnv/lib/python3.5/site-packages/majiq/src/basic_pipeline.py", line 29, in pipeline_run
    return pipeline.run()
  File "/mnt/data/heewlim/MLPT/RNAseq.mm10/Majiq/VirEnv/lib/python3.5/site-packages/majiq/src/build.py", line 278, in run
    self.builder(majiq_config)
  File "/mnt/data/heewlim/MLPT/RNAseq.mm10/Majiq/VirEnv/lib/python3.5/site-packages/majiq/src/build.py", line 316, in builder
    self.parse_denovo_elements(logger)
  File "/mnt/data/heewlim/MLPT/RNAseq.mm10/Majiq/VirEnv/lib/python3.5/site-packages/majiq/src/build.py", line 241, in parse_denovo_elements
    initargs=[find_new_junctions, self], maxtasksperchild=1)
  File "/usr/lib/python3.5/multiprocessing/context.py", line 118, in Pool
    context=self.get_context())
  File "/usr/lib/python3.5/multiprocessing/pool.py", line 167, in __init__
    raise ValueError("Number of processes must be at least 1")
ValueError: Number of processes must be at least 1

[Jordi Vaquero]

Can you send me the config file you are using?

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[Heewoong Lim]

Hi Jordi:

Here is my build.conf file.

samples are unstranded so I didn't set the strandedness or library type.

Thank you for your help.

[info]
readlen=100
samdir=../1.Align.link/
genome=mm10
genome_path=~/Research/Common_Data/mm10/genome/
[experiment]
Group1=sample11,sample12
Group2=sample21,sample22

[Jordi Vaquero]

Hello, 

Did you check the error file? If majiq was run in the cluster it should be a .err or something similar. 

The problems seems to be that majiq is not finding any of the samples. Since the samdir is a relative path, that can be a problem in a cluster based execution. 

Try changing the samdir to a global path and check the error files.

Thanks 

Jordi

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[Heewoong Lim]

Hi Jordi:

I am running it in my local machine with virtual environment on python 3.5.

So I only get majiq.log file, which doesn't have any more detail than the python error message that I posted.

I tried changing the samdir to absolute path but the results was the same.

- Lim

[Jordi Vaquero]

Ohh, just found your problem, in the config file you wrote [experiment] it should be plural, [experiments]. 

I will make an small check to be more descriptive on that error. 

Jordi

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[Heewoong Lim]

Hi Jordi:

OMG, it seems to be working.

Now it prints extra lines before all the running message (suggesting that it founds files ?)

2 1
2 1

And it is reading bam files now.

Thanks a lot for your help.

- Lim