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Jwindler / AutoHiC

A novel genome assembly pipeline based on deep learning
MIT License
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usage of autohic: Extending AutoHiC to other assembly software #28

Open hylu-coder opened 2 days ago

hylu-coder commented 2 days ago

Hi, Sorry for bothering you again. I'v already installed autohic sucessfully. I tested it on previous hic file generated by 3D-DNA. An error was returned: File C22.p_ctg.final.hic cannot be opened for reading. I guess that the HiC files generated by 3D-DNA may require some further processing before they can be fully utilized.

Thank you

Jwindler commented 2 days ago

Thanks for your feedback. Please provide me your installation log file so that I can check it for you. According to your description, your problem may be that Juicer or 3D-DNA is not running properly.

hylu-coder commented 1 day ago

Thanks for your reply. I can open the hic file in Juicer-box. The installation-related screen output is in the attached file. autohic.log

Jwindler commented 1 day ago

Your installation process is correct. can you give me your run autohic log file, thanks.

hylu-coder commented 23 hours ago

Sorry I wrote a incorrect HiC file path in my previous command. After re-running onehic, a new error was returned: Traceback (most recent call last): File "/data5/home/zqiang/AutoHiC/onehic.py", line 18, in from src.common.error_pd import infer_error File "/data5/home/zqiang/AutoHiC/src/common/error_pd.py", line 17, in import cv2 File "/data5/home/zqiang/.conda/envs/autohic/lib/python3.9/site-packages/cv2/init.py", line 181, in bootstrap() File "/data5/home/zqiang/.conda/envs/autohic/lib/python3.9/site-packages/cv2/init.py", line 153, in bootstrap native_module = importlib.import_module("cv2") File "/data5/home/zqiang/.conda/envs/autohic/lib/python3.9/importlib/init.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) ImportError: dlopen: cannot load any more object with static TLS

Jwindler commented 22 hours ago

so sorry to tell you, i have not encountered this error. you can refer to https://github.com/pytorch/pytorch/issues/2575 and https://github.com/scikit-learn/scikit-learn/issues/14485. in my opinion, you can use docker to solve it. maybe you should reinstall AutoHiC.