portcullis::FileSystemError*

[Xiaofei-git]

Dear there,

It gives the error message below when trying to run portcullis --help.

$ portcullis full --help
../lib/include/portcullis/portcullis_fs.hpp(158): Throw in function portcullis::PortcullisFS::PortcullisFS(const char*)
Dynamic exception type: boost::exception_detail::clone_implportcullis::FileSystemException
std::exception::what: std::exception
[portcullis::FileSystemError*] = Could not find suitable directory containing Portcullis data files at the expected location: /mnt/grid/sonas-hs/ware/hpc/home/xwang/anaconda3/share/portcullis

Basically “/sonas-hs/it/hpc/data” is a symbolic link to “/mnt/grid/it/hpc/data/data”, but somehow “/mnt/grid” is being put in the fron opf the symbolic link path.

I think I see a similar (might be similar) issue in this thread with a docker version installation #33

Could you help me out?

Thanks a lot!

BEST,

Xiaofei

[lucventurini]

Hi @swarbred, is there anyone that could have time to have a look at this while we are tied up with BBR?

[Xiaofei-git]

@swarbred @lucventurini
Actually, we can run it by giving the path, but the problem is I encountered an error for "filt" step, here is the log file below. We do have 'pandas' module, but it complained it is not found, even though it is there.

../lib/include/portcullis/python_helper.hpp(167): Throw in function void portcullis::PyHelper::execute(s
td::__cxx11::string, int, char**)
Dynamic exception type: boost::exception_detail::clone_implportcullis::PortcullisPythonException
std::exception::what: std::exception
[portcullis::PortcullisPythonError*] = Unexpected python error
Traceback (most recent call last):
File "//mnt/grid/it/hpc/data/data/bnb/portcullis/share/portcullis/scripts/portcullis/rule_filter.py",
line 8, in
from pandas import DataFrame
ModuleNotFoundError: No module named 'pandas'

[goeckeritz]

Hi, I hit a similar issue when trying to install with bioconda in a conda environment. Was this ever solved?

[lucventurini]

Hi @goeckeritz

I just tried with

conda install -c bioconda -y portcullis
portcullis full --help

without errors (Ubuntu 20.04 as Windows Subsystem Linux).

May I ask which version of portcullis is giving you trouble and on which OS please?

Kind regards

[goeckeritz]

Hi @lucventurini,

Thanks so much for the quick response. Our operating system is CentOS 7. My sequence of commands was

conda create -n portcullis
conda install portcullis --channel=bioconda

Then when I did
portcullis full --help

It printed:
../lib/include/portcullis/portcullis_fs.hpp(158): Throw in function portcullis::PortcullisFS::PortcullisFS(const char*)
Dynamic exception type: boost::wrapexceptportcullis::FileSystemException
std::exception::what: std::exception
[portcullis::FileSystemError*] = Could not find suitable directory containing Portcullis data files at the expected location: /mnt/mnt/home/goeckeri/miniconda3/envs/portcullis/share/portcullis

Now that I'm looking at this again, looks like the /mnt/mnt/..... is a little weird. Like portcullis is looking place. Should just be one /mnt/ in the directory.

I also tried to install it from source at that point but our hpcc has all sorts of odd dependency issues with compilers... in the end I asked our staff to install it for me (which they did) and it's working fine now. So I should be good (sorry to those who may have this problem in the future!).

Thanks again,
Charity

[lucventurini]

Dear @goeckeritz

Thank you for the expansive feedback. We will try to look into that in the future ... but, may I ask, does your HPC have a non-standard implementation of the home directory? As you noticed yourself the extra /mnt is odd.