Error when run base call step

adaxidedakaonang commented 5 years ago

Whern I run base call step, I get such error: AttributeError: 'Namespace' object has no attribute 'polya' my command is : python chiron/entry.py call -i input -o output -m model input and model are folders which save fast5_file, model_file, respectively. Output is a empty folder.

the complete error is: ` Traceback (most recent call last): File "chiron/entry.py", line 154, in main() File "chiron/entry.py", line 146, in main args.func(args) File "chiron/entry.py", line 38, in evaluation extract(FLAGS) File "/home/ubuntu/ADAXI/Gene/Chiron/chiron/utils/extract_sig_ref.py", line 61, in extract if FLAGS.polya is not None: AttributeError: 'Namespace' object has no attribute 'polya'

` I use python2.7, tensorflow1.14 my package is:

packages in environment at /home/ubuntu/.conda/envs/chiron:

Name Version Build Channel _libgcc_mutex 0.1 main defaults _tflow_select 2.1.0 gpu defaults absl-py 0.8.0 py27_0 defaults astor 0.8.0 py27_0 defaults backports 1.0 py_2 defaults backports.weakref 1.0.post1 py_1 defaults biopython 1.74 blas 1.0 mkl defaults c-ares 1.15.0 h7b6447c_1001 defaults ca-certificates 2019.10.16 0 defaults certifi 2019.9.11 py27_0 defaults chiron 0.5.1 cudatoolkit 10.1.168 0 defaults cudnn 7.6.0 cuda10.1_0 defaults cupti 10.1.168 0 defaults enum34 1.1.6 py27_1 defaults funcsigs 1.0.2 py27_0 defaults future 0.17.1 py27_0 defaults futures 3.3.0 py27_0 defaults gast 0.3.2 py_0 defaults google-pasta 0.1.7 py_0 defaults grpcio 1.16.1 py27hf8bcb03_1 defaults h5py 2.9.0 py27h7918eee_0 defaults hdf5 1.10.4 hb1b8bf9_0 defaults intel-openmp 2019.4 243 defaults keras-applications 1.0.8 py_0 defaults keras-preprocessing 1.1.0 py_1 defaults libedit 3.1.20181209 hc058e9b_0 defaults libffi 3.2.1 hd88cf55_4 defaults libgcc-ng 9.1.0 hdf63c60_0 defaults libgfortran-ng 7.3.0 hdf63c60_0 defaults libprotobuf 3.9.2 hd408876_0 defaults libstdcxx-ng 9.1.0 hdf63c60_0 defaults linecache2 1.0.0 py27_0 defaults markdown 3.1.1 py27_0 defaults mkl 2019.4 243 defaults mkl-service 2.3.0 py27he904b0f_0 defaults mkl_fft 1.0.14 py27ha843d7b_0 defaults mkl_random 1.1.0 py27hd6b4f25_0 defaults mock 3.0.5 py27_0 defaults ncurses 6.1 he6710b0_1 defaults numpy 1.16.5 py27h7e9f1db_0 defaults numpy-base 1.16.5 py27hde5b4d6_0 defaults openssl 1.1.1d h7b6447c_3 defaults packaging 19.2 pandas 0.23.0 patsy 0.5.1 pip 19.3.1 py27_0 defaults protobuf 3.9.2 py27he6710b0_0 defaults pyparsing 2.4.2 python 2.7.17 h9bab390_0 defaults python-dateutil 2.8.0 pytz 2019.3 readline 7.0 h7b6447c_5 defaults scipy 1.2.1 py27h7c811a0_0 defaults setuptools 41.4.0 py27_0 defaults six 1.12.0 py27_0 defaults sqlite 3.30.0 h7b6447c_0 defaults statsmodels 0.10.1 tensorboard 1.14.0 py27hf484d3e_0 defaults tensorflow 1.14.0 gpu_py27h39f1c70_0 defaults tensorflow-base 1.14.0 gpu_py27he45bfe2_0 defaults tensorflow-estimator 1.14.0 py_0 defaults tensorflow-gpu 1.14.0 h0d30ee6_0 defaults termcolor 1.1.0 py27_1 defaults tk 8.6.8 hbc83047_0 defaults tqdm 4.36.1 traceback2 1.4.0 py27_0 defaults unittest2 1.1.0 py27_0 defaults werkzeug 0.16.0 py_0 defaults wheel 0.33.6 py27_0 defaults wrapt 1.11.2 py27h7b6447c_0 defaults zlib 1.2.11 h7b6447c_3 defaults

I need your help!Thanks!

adaxidedakaonang commented 5 years ago

I meet the same question when I run test step. It may be a python question, but I use python2.7 which is same version as yours.

adaxidedakaonang commented 5 years ago

When I change environment to py3 and tensorflow1.14, the mistake is still exits. 唉……

haotianteng commented 5 years ago

Fixed. I will close it if you still encounter problems please don't hesitate to follow up and leave a message.

haotianteng / Chiron

Error when run base call step #96