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Illegal instruction while running kmer-db #22

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gracegyho opened this issue Oct 19, 2023 · 1 comment
Open

Illegal instruction while running kmer-db #22

gracegyho opened this issue Oct 19, 2023 · 1 comment

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@gracegyho
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Hi there,

I am actually running kmer-db as a part of SqueezeMeta's dependencies, but even when I do a fresh install via conda in a new environment (versions 1.11.1, 1.7.6, or 1.9.2), and run kmer-db command, I get the error message "Illegal instruction".

I am running on an institute server running Debian 4.19.289-2... Not sure what else is relevant here.

I even tried installing the binary from the tarball, running make, and the executable kmer-db is also throwing the same error.

@gracegyho
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Maybe this additional message after installing v 1.11.1 might shed light on the issue I'm facing:

Channels:
 - bioconda
 - conda-forge
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/gho/miniconda3/envs/kmer-db-v1-11-1

  added / updated specs:
    - kmer-db=1.11.1


The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge 
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-2_gnu 
  kmer-db            bioconda/linux-64::kmer-db-1.11.1-hdcf5f25_2 
  libgcc-ng          conda-forge/linux-64::libgcc-ng-13.2.0-h807b86a_2 
  libgomp            conda-forge/linux-64::libgomp-13.2.0-h807b86a_2 
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-13.2.0-h7e041cc_2 
  libzlib            conda-forge/linux-64::libzlib-1.2.13-hd590300_5 
  zlib               conda-forge/linux-64::zlib-1.2.13-hd590300_5 


Proceed ([y]/n)? y


Downloading and Extracting Packages

Preparing transaction: done
Verifying transaction: - 
SafetyError: The package for kmer-db located at /home/gho/miniconda3/pkgs/kmer-db-1.11.1-hdcf5f25_2
appears to be corrupted. The path 'bin/kmer-db'
has an incorrect size.
  reported size: 484392 bytes
  actual size: 501880 bytes


done
Executing transaction: done

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