Error message: Please inupt a reference file

[lvbakker]

Hi,
I am running BioNanoAnalyst in a unix environment but i cannot get it to work.
I started the application: Python App.py in a virtual env with all python dependencies installed.
The application starts and I want to do a test run with the provided test set in the /data folder.
I selected the reference (fasta) and the three files for option 2 that were provided and provided a confidence score.
But i keep seeing this message when i press Analyse:

"Please input a reference file !"
Can someone explain what seems to be going wrong?
Thanks!
with regards, Linda

[yyx8671]

Hi Linda,

Which python did you use? and have you checked your fasta file (please ensure it is a proper fasta file)?

Cheers,
Andy

[lvbakker]

Hi Andy,
I am using a vitual env with Python 2.7.12.
I selected for a reference, the fasta file that was present in the data dir:

When i press Analyse, it shows me the above mentioned message

thanks, Linda

[yyx8671]

Hi Linda,
From your screenshots, it seems the BioNanoAnalyst didn't work properly on your server. The code such as "u'sequences(*fasta *fa *fna)" should not appear.
May I ask which PyQt did you use? BioNanoAnalyst requests PyQt4 or PySide.
Cheers,
Andy

[lvbakker]

The python package that was installed is PySide-1.2.4

[yyx8671]

Can you try to install anaconda python2 (https://www.anaconda.com/download/) and try to run BioNanoAnalyst using anaconda python?

[bwlang]

I see the same problem on my system.

Here is the conda env to reproduce the problem:
I had to manually install Image using pip install Image

# $ conda create --name <env> --file <this file>
# platform: linux-64
@EXPLICIT
https://repo.continuum.io/pkgs/main/linux-64/ca-certificates-2017.08.26-h1d4fec5_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/intel-openmp-2018.0.0-hc7b2577_8.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/libgcc-ng-7.2.0-h7cc24e2_2.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/libgfortran-ng-7.2.0-h9f7466a_2.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/libstdcxx-ng-7.2.0-h7a57d05_2.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/expat-2.2.5-he0dffb1_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/icu-58.2-h9c2bf20_1.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/jpeg-9b-h024ee3a_2.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/libffi-3.2.1-hd88cf55_4.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/libxcb-1.12-hcd93eb1_4.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/mkl-2018.0.1-h19d6760_4.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/ncurses-6.0-h9df7e31_2.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/openssl-1.0.2n-hb7f436b_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/pcre-8.41-hc27e229_1.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/tk-8.6.7-hc745277_3.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/xz-5.2.3-h55aa19d_2.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/zlib-1.2.11-ha838bed_2.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/glib-2.53.6-h5d9569c_2.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/libedit-3.1-heed3624_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/libpng-1.6.32-hbd3595f_4.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/libtiff-4.0.9-h28f6b97_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/libxml2-2.9.4-h2e8b1d7_6.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/readline-7.0-ha6073c6_4.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/dbus-1.10.22-h3b5a359_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/freetype-2.8-hab7d2ae_1.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/gstreamer-1.12.2-h4f93127_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/sqlite-3.20.1-hb898158_2.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/fontconfig-2.12.4-h88586e7_1.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/gst-plugins-base-1.12.2-he3457e5_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/python-2.7.14-h1571d57_29.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/backports-1.0-py27h63c9359_1.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/backports_abc-0.5-py27h7b3c97b_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/certifi-2017.11.5-py27h71e7faf_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/functools32-3.2.3.2-py27h4ead58f_1.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/msgpack-python-0.5.1-py27h6bb024c_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/numpy-1.14.0-py27h3dfced4_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/olefile-0.44-py27h4bd3e3c_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/pyparsing-2.2.0-py27hf1513f8_1.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/pytz-2017.3-py27h001bace_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/qt-5.6.2-h974d657_12.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/sip-4.18.1-py27he9ba0ab_2.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/six-1.11.0-py27h5f960f1_1.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/subprocess32-3.2.7-py27h373dbce_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/cycler-0.10.0-py27hc7354d3_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/django-1.11.8-py27hd476221_0.tar.bz2
https://conda.anaconda.org/bioconda/linux-64/mmtf-python-1.0.2-py27_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/pillow-5.0.0-py27h3deb7b8_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/pyqt-5.6.0-py27h4b1e83c_5.tar.bz2
https://conda.anaconda.org/bioconda/linux-64/python-dateutil-2.3-py27_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/setuptools-38.4.0-py27_0.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/shiboken-1.2.1-py27_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/singledispatch-3.4.0.3-py27h9bcb476_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/ssl_match_hostname-3.5.0.1-py27h4ec10b9_2.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/backports.functools_lru_cache-1.4-py27he8db605_1.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/pandas-0.22.0-py27hf484d3e_0.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/pyside-1.2.0-py27_0.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/reportlab-3.4.0-py27_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/tornado-4.5.3-py27_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/wheel-0.30.0-py27h2bc6bb2_1.tar.bz2
https://conda.anaconda.org/bioconda/linux-64/biopython-1.68-py27_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/matplotlib-2.1.1-py27h0128e01_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/pip-9.0.1-py27ha730c48_4.tar.bz2

[bwlang]

I tried using pyQT4 instead of pyside - which worked:
here's the env:

# This file may be used to create an environment using:
# $ conda create --name <env> --file <this file>
# platform: linux-64
@EXPLICIT
https://repo.continuum.io/pkgs/main/linux-64/ca-certificates-2017.08.26-h1d4fec5_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/intel-openmp-2018.0.0-hc7b2577_8.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/libgcc-ng-7.2.0-h7cc24e2_2.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/libgfortran-3.0.0-1.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/libgfortran-ng-7.2.0-h9f7466a_2.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/libiconv-1.14-0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/libstdcxx-ng-7.2.0-h7a57d05_2.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/expat-2.2.5-he0dffb1_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/icu-58.2-h9c2bf20_1.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/jpeg-9b-h024ee3a_2.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/libffi-3.2.1-hd88cf55_4.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/libxcb-1.12-hcd93eb1_4.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/mkl-2018.0.1-h19d6760_4.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/ncurses-6.0-h9df7e31_2.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/openblas-0.2.14-4.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/openssl-1.0.2n-hb7f436b_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/pcre-8.41-hc27e229_1.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/pixman-0.34.0-hceecf20_3.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/tk-8.6.7-hc745277_3.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/xz-5.2.3-h55aa19d_2.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/zlib-1.2.11-ha838bed_2.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/glib-2.53.6-h5d9569c_2.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/libedit-3.1-heed3624_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/libpng-1.6.32-hbd3595f_4.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/libtiff-4.0.9-h28f6b97_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/libxml2-2.9.4-h2e8b1d7_6.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/readline-7.0-ha6073c6_4.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/dbus-1.10.22-h3b5a359_0.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/freetype-2.5.5-2.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/gstreamer-1.12.2-h4f93127_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/sqlite-3.20.1-hb898158_2.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/fontconfig-2.12.1-3.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/gst-plugins-base-1.12.2-he3457e5_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/python-2.7.14-h1571d57_29.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/backports-1.0-py27h63c9359_1.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/backports_abc-0.5-py27h7b3c97b_0.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/cairo-1.14.8-0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/certifi-2017.11.5-py27h71e7faf_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/functools32-3.2.3.2-py27h4ead58f_1.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/msgpack-python-0.5.1-py27h6bb024c_0.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/numpy-1.10.2-py27_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/olefile-0.44-py27h4bd3e3c_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/pyparsing-2.2.0-py27hf1513f8_1.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/pytz-2017.3-py27h001bace_0.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/qt-4.8.7-3.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/sip-4.18-py27_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/six-1.11.0-py27h5f960f1_1.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/subprocess32-3.2.7-py27h373dbce_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/cycler-0.10.0-py27hc7354d3_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/django-1.11.8-py27hd476221_0.tar.bz2
https://conda.anaconda.org/bioconda/linux-64/mmtf-python-1.0.2-py27_0.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/pillow-4.2.1-py27_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/pycairo-1.13.3-py27hea6d626_0.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/pyqt-4.11.4-py27_4.tar.bz2
https://conda.anaconda.org/bioconda/linux-64/python-dateutil-2.3-py27_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/setuptools-38.4.0-py27_0.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/shiboken-1.2.1-py27_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/singledispatch-3.4.0.3-py27h9bcb476_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/ssl_match_hostname-3.5.0.1-py27h4ec10b9_2.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/backports.functools_lru_cache-1.4-py27he8db605_1.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/matplotlib-1.5.1-np110py27_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/pandas-0.21.1-py27h38cdd7d_0.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/reportlab-3.4.0-py27_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/tornado-4.5.3-py27_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/wheel-0.30.0-py27h2bc6bb2_1.tar.bz2
https://conda.anaconda.org/bioconda/linux-64/biopython-1.68-py27_0.tar.bz2
https://repo.continuum.io/pkgs/main/linux-64/pip-9.0.1-py27ha730c48_4.tar.bz2