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PacificBiosciences / kineticsTools

Tools for detecting DNA modifications from single molecule, real-time sequencing data
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ImportError: No module named pyBigWig #70

Open liufeibio opened 4 years ago

liufeibio commented 4 years ago

Hi, there I run the ipdsummary programme, but got an error: ImportError: No module named pyBigWig. I have installed it via conda, but still got this error. Could you help me with it? Thanks! This is the running: ipdSummary ./raw.bam --reference ../quickmerge/merged.pyscaf.fasta --gff basemods.gff --csv kinetics.csv --bigwig IpdRatio.bw --identify m6A,m4C,m5C_TET --methylFraction --numWorkers 10 --minCoverage 3 this is error indicated: Process KineticsWriter-11: Traceback (most recent call last): File "/usr/lib/python2.7/multiprocessing/process.py", line 267, in _bootstrap self.run() File "/usr/lib/python2.7/dist-packages/kineticsTools/ResultWriter.py", line 112, in run self._run() File "/usr/lib/python2.7/dist-packages/kineticsTools/ResultWriter.py", line 70, in _run self.onStart() File "/usr/lib/python2.7/dist-packages/kineticsTools/ResultWriter.py", line 941, in onStart sinkList.append(func(name)) File "/usr/lib/python2.7/dist-packages/kineticsTools/pipelineTools.py", line 35, in start next(c) File "/usr/lib/python2.7/dist-packages/kineticsTools/ResultWriter.py", line 284, in bigWigConsumer import pyBigWig ImportError: No module named pyBigWig Child process exited with exitcode=1. Aborting. 2019-12-11 12:43:20,630 [ERROR] Child process exited with exitcode=1. Aborting.

rhallPB commented 4 years ago

Have you tried installing pybigwig independently? conda install -c bioconda pybigwig

liufeibio commented 4 years ago

yes, I have tried that

natechols commented 4 years ago

I don't understand how this error can happen if you have actually installed the module. What happens when you run python -c "import pyBigWig", using the bioconda python?

rhallPB commented 4 years ago

I notice the install is in your system path, you may want to try installing and running everything in a fresh conda environment, https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html

liufeibio commented 4 years ago

I don't understand how this error can happen if you have actually installed the module. What happens when you run python -c "import pyBigWig", using the bioconda python?

it is like this:

(pbalign) sujitmaiti@sujitmaiti-MS-7885:~/biosoftware/kineticsTools$ python
Python 2.7.15 | packaged by conda-forge | (default, Nov 29 2018, 06:43:57)
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import pyBigWig
>>>
natechols commented 4 years ago

I think @rhallPB has the right idea, you may have installed kineticsTools into the wrong Python.

liufeibio commented 4 years ago

I think @rhallPB has the right idea, you may have installed kineticsTools into the wrong Python.

I am creating a new conda environment for kineticsTools with python=2.7, am I using a right version of python? Thanks!

liufeibio commented 4 years ago

I think @rhallPB has the right idea, you may have installed kineticsTools into the wrong Python.

I am creating a new conda environment for kineticsTools with python=2.7, am I using a right version of python? Thanks!

I found that the code (print(delim.join(cols), file=f)) in ResultsWriter.py seems to be written in Python3? So I should use python3? Thanks for your answer.

natechols commented 4 years ago

No, because it's a compatibility function for Python 2: https://github.com/PacificBiosciences/kineticsTools/blob/master/kineticsTools/ResultWriter.py#L1 The next release of kineticsTools will switch to Python 3, however. (No, I don't have an ETA for this.)