Bruno Hinckel

I also tried this i.e. without creating a virtual environment though it did not work. I downloaded the same pipeline from another location, which looks slightly different, and it now...

Same here, I have tried few things, some of which worked partially, as described [here](https://github.com/nanoporetech/pipeline-structural-variation/issues/5)

I have found the same pipeline from nanopore, though [hosted elsewhere](https://community.nanoporetech.com/knowledge/bioinformatics/structural-variation-analy-5068/tutorial) that works on their sample data set. Here's the link to the [github page](https://github.com/nanoporetech/ont_tutorial_sv)

below is the message from Python Language Sever: ``` Traceback (most recent call last): File "/home/ngs/.vscode-server/extensions/ms-python.python-2022.16.0/pythonFiles/run-jedi-language-server.py", line 9, in from jedi_language_server.cli import cli File "/home/ngs/.vscode-server/extensions/ms-python.python-2022.16.0/pythonFiles/lib/jedilsp/jedi_language_server/cli.py", line 7, in from .server...

thanks for the reply. I work on multiple VS code workspaces, and I also get this error when the python interpreter is 3.7.3. Also it is odd that these collapse...

actually it works now that I changed the language server to pylance, I am not a huge fan of this extension though

> > @GiveMePseudonyms do you get the same traceback that @BCArg posted when using Python 3.10? > > Please forgive my ignorance @pappasam but how do I find the traceback...

thanks for the quick reply. I did manually install `seqkit` and copied the executable to `/usr/local/bin`, according to the instructions Also following your suggestion I copied `seqkit` to `/home/bhinckel/git/pomoxis/venv/bin/`, as...

I just called `seqkit fq2fa MinIonRun1/guppy/*.fastq` from the command line and it works. I have also put the directories under `~/git/pomoxis/venv/bin/activate/pomoxis-0.3.4-py_0` directly under `~/git/pomoxis/venv/bin/activate/` i.e. ``` (katuali) bhinckel@Brightcore-testsrv:~$ ll /home/bhinckel/git/pomoxis/venv/bin/activate/...

HI Maria, thanks for the quick reply Unfortunately I cannot use the only version for our samples, even though that I, for one, know that the input files will not...