Open alexahess opened 1 year ago
This looks like a weird conda issue, how exactly have you installed conda and what is the exact command you used to install the pipeline?
I have installed anaconda by downloading the installer and following the instruction found here: https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html. I had issues installing the pipeline through conda and therefore followed the instructions on installation via source, which I followed to the letter.
When I try to install via conda I get the following error:
$ conda install -c bioconda -c conda-forge artic
Retrieving notices: ...working... done
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: |
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed
UnsatisfiableError: The following specifications were found to be incompatible with each other:
Output in format: Requested package -> Available versionsThe following specifications were found to be incompatible with your system:
- feature:/linux-64::__glibc==2.35=0
- feature:|@/linux-64::__glibc==2.35=0
Your installed version is: 2.35
Hello, I also encountered the following problems, may I ask if you have solved them
$/path/to/leafcutter-master/scripts/bam2junc.sh SRR12705760.bam samtools: /work/home//miniconda3/bin/../lib/libtinfo.so.6: no version information available (required by samtools) samtools: /work/home//miniconda3/bin/../lib/libncurses.so.6: no version information available (required by samtools)
my samtools version is 1.16.1
I found that this doesn't seem to affect usage, so I'd like to ask if this bug will have any impact if it's not fixed
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Hello,
I've installed the pipeline on a new computer, using ubuntu 22.04.2. However, when I try to run the pipeline, the steps using samtools and BCFtools fails. I'm using the 1.2.3 version of the Artic pipeline.
The errors I get for samtools are:
This error does not happen when I run samtools 1.16, only for 1.15 which is part of the environment.
and for BCFtools
Do you have any idea of how to fix this?
Regards, Alexander