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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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singularity HiC-Pro_2.11.3-beta/bin/../scripts//Makefile:191: recipe for target 'ice_norm' failed #298

Open amagli opened 4 years ago

amagli commented 4 years ago

Dear Nicholas, First of all, happy 2020 :)

I have been attempting to run the latest singularity image but I am encountering a few issues: 1) analysis of the test dataset completes with no errors but the directories in hic_results/matrix/iced are empty. Is it just because the number of reads is just very small?

2) this is more critical. I have attempted to run the latest image (hicpro_devel_ubuntu.img) using my data and the analysis stops at the ICE normalization with this error:

Mon Dec 30 23:01:41 CST 2019 Run ICE Normalization ... Logs: logs/plusdox_B/ice_10000.log /usr/local/bin/HiC-Pro_2.11.3-beta/bin/../scripts//Makefile:191: recipe for target 'ice_norm' failed make: *** [ice_norm] Error 1

I was looking at the previous reported issues (https://github.com/nservant/HiC-Pro/issues/231) and it seems there was a problem with the installation of iced in the root local python dir. I tried to do this (see below): $ singularity exec hicpro_devel_ubuntu.img python $ import iced and I got this result:

$ singularity exec hicpro_devel_ubuntu.img python Python 2.7.11 |Continuum Analytics, Inc.| (default, Jun 15 2016, 15:21:30) [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2 Type "help", "copyright", "credits" or "license" for more information. Anaconda is brought to you by Continuum Analytics. Please check out: http://continuum.io/thanks and https://anaconda.org $ import iced Traceback (most recent call last): File "", line 1, in File "/home/perlinge/amagli/.local/lib/python2.7/site-packages/iced/init.py", line 1, in from . import normalization File "/home/perlinge/amagli/.local/lib/python2.7/site-packages/iced/normalization.py", line 3, in from .normalization import _update_normalization_csr ImportError: /home/perlinge/amagli/.local/lib/python2.7/site-packages/iced/normalization.so: undefined symbol: PyUnicodeUCS2_Format

Do you have an idea of what could be the problem? Thank you very much, Alessandro

nservant commented 4 years ago

Hi Alessandro Thanks for reporting this issue. I will try to generate a new image and come back to you best

nservant commented 4 years ago

Hi Alessandro,

I just build a new Singularity image at http://zerkalo.curie.fr/partage/HiC-Pro/singularity_images/hicpro_2.11.3_ubuntu.img Hope it helps Nicolas

$ singularity exec hicpro_2.11.3_ubuntu.img python
Python 2.7.15 | packaged by conda-forge | (default, Mar  5 2020, 14:56:06) 
[GCC 7.3.0] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import iced
>>>
amagli commented 4 years ago

Thank you very much Nicolas.

Best, Alessandro