no version information available (required by samtools)

[alexahess]

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:

samtools: /home/miks/mambaforge/envs/artic/bin/../lib/libtinfow.so.6: no version information available (required by samtools)
samtools: /home/miks/mambaforge/envs/artic/bin/../lib/libncursesw.so.6: no version information available (required by samtools)
samtools: /home/miks/mambaforge/envs/artic/bin/../lib/libncursesw.so.6: no version information available (required by samtools)

This error does not happen when I run samtools 1.16, only for 1.15 which is part of the environment.

and for BCFtools

bcftools: error while loading shared libraries: libgsl.so.25: cannot open shared object file: No such file or directory

Do you have any idea of how to fix this?

Regards,
Alexander

[BioWilko]

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?

[alexahess]

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

[Fight-a-tiger-in-the-mountain]

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

[JiachenWang-wjc]

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

[Fight-a-tiger-in-the-mountain]

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