error at draft assembly stage

[madhubioinfo]

Iam trying to run HINGE on my pacbio dataset , when am running draft-path, am getting the following error from pbcore.io import FastaIO ModuleNotFoundError: No module named 'pbcore'

I tried installing by looking at this page https://github.com/PacificBiosciences/pbcore/issues/9 still the HINGE assembler is giving me the same error, please help me to solve this issue

[fxia22]

Thanks for reporting. What will happen if you run python and run from pbcore.io import FastaIO? You can verify pbcore is installed properly.

[fxia22]

btw, are you using python3 or python2.7?

[govinda-kamath]

Were you able to sort this out @madhubioinfo ?

[madhubioinfo]

sorry I couldn't get back to this issue , it was due to version of python and thanks for addressing my issue

[fxia22]

Thanks for your feedback.

[mictadlo]

Hi, I installed Hinge as described but it has failed with ImportError: No module named pbcore.io it seems that the library is missing:

> source utils/setup.sh
> python
Python 2.7.13 (default, Jul 21 2017, 16:25:46) 
[GCC 6.3.0] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from pbcore.io import FastaIO
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: No module named pbcore.io
>>> 

What did I miss?

Thank you in advance

MIchal

[govinda-kamath]

HI Mlchal,

You need to install pbcore. You can do it using pip. I've updated the reqs.

[govinda-kamath]

You can also install by using pip install -r requirements.txt using this as requirements.txt.

[mictadlo]

Thank you, it works now. it would be good to have that file also in this repository.