undefined symbol: hts_utell

[RADIOMUMM]

I use the commad ""/usr/bin/basevar" -h",but it dosnt work !

return me "undefined symbol: hts_utell"

whole waring:
Traceback (most recent call last):
File "/usr/bin/basevar", line 9, in
load_entry_point('basevar==0.8.0', 'console_scripts', 'basevar')()
File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 378, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 2566, in load_entry_point
return ep.load()
File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 2260, in load
entry = import(self.module_name, globals(),globals(), ['name'])
File "/usr/lib64/python2.7/site-packages/basevar/runner.py", line 13, in
from caller.executor import BaseTypeRunner
File "basevar/caller/executor.pyx", line 1, in init basevar.caller.executor
"""
File "basevar/io/fasta.pyx", line 8, in init basevar.io.fasta
from basevar.io.openfile import Open
File "basevar/io/openfile.pyx", line 11, in init basevar.io.openfile
from basevar.io.BGZF.bgzf import BGZFile
File "basevar/io/BGZF/bgzf.pyx", line 1, in init basevar.io.BGZF.bgzf
# cython: embedsignature=True
ImportError: /usr/lib64/python2.7/site-packages/basevar/io/htslibWrapper.so: undefined symbol: hts_utell

[xiaoliangtian]

hi, i had the same problem. please tell me how it was finally resolved.

[RADIOMUMM]

hi, i had the same problem. please tell me how it was finally resolved.
hi
i give up this software!
You can try this BaseVarC

[Sondr11]

@RADIOMUMM
Can you help me how to install BaseVarC?

[RADIOMUMM]

@RADIOMUMM Can you help me how to install BaseVarC?

move to BaseVarC github page (BaseVarC)

git clone --recursive https://github.com/Zilong-Li/BaseVarC.git
cd BaseVarC
./configure
make

[Sondr11]

Hi @RADIOMUMM
I installed and run test success. Now I will run for sample, Hope it's OK.
Beside,can you guide me how to interpret these millions of variants as pathogenic, benign or like begin?
Thank you so much

[Velcon-Zheng]

hi, i had the same problem. please tell me how it was finally resolved.
hi
i give up this software!
You can try this BaseVarC

I've successfully installed basevar 0.8.0. Below are the versions of the related dependencies that I have installed:

• htslib: 1.9
  • This was crucial for resolving the aforementioned error.
• openssl: 1.0.2k
  • Need to create symbolic links:
    • libcrypto.so.10 -> lib/libcrypto.so.1.0.0
    • libssl.so.10 -> lib/libssl.so.1.0.0
  • This was crucial for resolving the aforementioned error.
• certifi: 2019.11.28
• python: 2.7.15
• Cython: 0.29.6
• Logbook: 1.4.3.post1
• numpy: 1.15.4
• pip: 20.1.1
• pysam: 0.12.0.1
• scikit-learn: 0.20.2
• scipy: 1.2.3
• setuptools: 44.0.0.post20200102
• wheel: 0.37.1

export C_INCLUDE_PATH=/*/*/htslib_1.9/include:$C_INCLUDE_PATH
export LIBRARY_PATH=/*/*/htslib_1.9/lib
export LD_LIBRARY_PATH=/*/*/htslib_1.9/lib:/*/*/openssl_lib/

cd basevar-0.8.0/
python setup.py install