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YangLab / CIRCexplorer2

circular RNA analysis toolset
http://circexplorer2.readthedocs.org/
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ValueError while running align #48

Closed KasperThystrup closed 4 years ago

KasperThystrup commented 4 years ago

Hi I'm trying to set up an experimental run by following the guide posted at readthedocs.io, yet I get a valueerror when I execute the CIRCexplorer2 align with my bowtie2 index files:

python ~/miniconda3/pkgs/circexplorer2-2.3.8-pyh864c0ab_1/site-packages/circ2/align.py -G hg19_kg.gtf -j bowtie2_index -f RNA_seq.fastq > CIRCexplorer2_align.log

Traceback (most recent call last):
  File "home/ME/miniconda3/pkgs/circexplorer2-2.3.8-pyh864c0ab_1/site-packages/circ2/align.py", line 29, in <module>
    from .parse import tophat_fusion_parse
ValueError: Attempted relative import in non-package

I have set up the following Conda environment

# packages in environment at /home/ME/miniconda3/envs/circexplorer2:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main  
asn1crypto                1.4.0                      py_0  
bedtools                  2.29.2               hc088bd4_0    bioconda
blas                      1.0                         mkl  
bowtie2                   2.2.5            py27h6bb024c_5    bioconda
bzip2                     1.0.8                h7b6447c_0  
ca-certificates           2020.7.22                     0  
certifi                   2019.11.28               py27_0  
cffi                      1.14.0           py27he30daa8_1  
chardet                   3.0.4                 py27_1003  
circexplorer2             2.3.8              pyh864c0ab_1    bioconda
cryptography              2.3.1            py27hc365091_0  
cufflinks                 2.2.1                    py27_2    bioconda
docopt                    0.6.2                    py27_0    anaconda
enum34                    1.1.6                    py27_1  
idna                      2.10                       py_0  
intel-openmp              2020.2                      254  
ipaddress                 1.0.23                     py_0  
libedit                   3.1.20191231         h14c3975_1  
libffi                    3.3                  he6710b0_2  
libgcc                    7.2.0                h69d50b8_2  
libgcc-ng                 9.1.0                hdf63c60_0  
libgfortran-ng            7.3.0                hdf63c60_0  
libpng                    1.6.37               hbc83047_0  
libstdcxx-ng              9.1.0                hdf63c60_0  
libuuid                   1.0.3                h1bed415_2  
mkl                       2020.2                      256  
mkl-service               2.3.0            py27he904b0f_0  
mkl_fft                   1.0.15           py27ha843d7b_0  
mkl_random                1.1.0            py27hd6b4f25_0  
mysql-connector-c         6.1.11               hf4847fb_0  
ncurses                   6.2                  he6710b0_1  
numpy                     1.16.6           py27hbc911f0_0  
numpy-base                1.16.6           py27hde5b4d6_0  
openssl                   1.0.2u               h7b6447c_0  
pandas                    0.24.2           py27he6710b0_0  
perl                      5.26.2               h14c3975_0  
pip                       19.3.1                   py27_0  
pybedtools                0.8.1            py27he513fc3_0    bioconda
pycparser                 2.20                       py_2  
pyopenssl                 19.0.0                   py27_0  
pysam                     0.8.4                    py27_0    bioconda
pysocks                   1.7.1                    py27_0  
python                    2.7.18               h15b4118_1  
python-dateutil           2.8.1                      py_0  
pytz                      2020.1                     py_0  
readline                  8.0                  h7b6447c_0  
requests                  2.24.0                     py_0  
scipy                     1.1.0            py27hfa4b5c9_1    anaconda
setuptools                44.0.0                   py27_0  
six                       1.15.0                     py_0  
sqlite                    3.33.0               h62c20be_0  
tk                        8.6.10               hbc83047_0  
tophat                    2.1.1                    py27_3    bioconda
ucsc-bedgraphtobigwig     357                           1    bioconda
ucsc-bedtobigbed          357                           1    bioconda
ucsc-genepredtogtf        366                  h5eb252a_0    bioconda
ucsc-gtftogenepred        366                  h5eb252a_0    bioconda
urllib3                   1.25.7                   py27_0  
wheel                     0.35.1                     py_0  
xz                        5.2.5                h7b6447c_0  
zlib                      1.2.11               h7b6447c_3

Thank you for your time and help!

KasperThystrup commented 4 years ago

I can likewise add that I get an error at the same position when executing with system python3.5 inside the above listed environment. However, I'm not certain whether all dependencies are installed correctly for this version.

Traceback (most recent call last):
  File "/home/kasper/miniconda3/pkgs/circexplorer2-2.3.8-pyh864c0ab_1/site-packages/circ2/align.py", line 29, in <module>
    from .parse import tophat_fusion_parse
SystemError: Parent module '' not loaded, cannot perform relative import
kepbod commented 4 years ago

Can you try to reinstall CIRCexplorer from scratch to check whether this error still occurs?