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Issue created by Andrew@Krasnopeev

CondaVerificationError after installation

Hi,

I followed Installation guide step by step. But when I tried to run PathoFact got the error:

console output for test from guide 

(PathoFact) anri@anriPC:/media/anri/FAE8F3E0E8F39959/PathoFact-master$ snakemake -s test/Snakefile --use-conda --reason --cores 4 -p
Building DAG of jobs...
Executing subworkflow pathofact.
Building DAG of jobs...
Creating conda environment envs/VirSorter.yaml...
Downloading remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /media/anri/FAE8F3E0E8F39959/PathoFact-master/rules/AMR/../../envs/VirSorter.yaml:
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

Downloading and Extracting Packages
libcurl-7.69.1       | 573 KB    | ########## | 100% 
libedit-3.1.20170329 | 172 KB    | ########## | 100% 
entrez-direct-13.3   | 4.7 MB    | ########## | 100% 
perl-moose-2.2011    | 444 KB    | ########## | 100% 
perl-class-method-mo | 13 KB     | ########## | 100% 
perl-module-implemen | 9 KB      | ########## | 100% 
perl-mro-compat-0.13 | 10 KB     | ########## | 100% 
perl-getopt-long-2.5 | 27 KB     | ########## | 100% 
perl-package-stash-0 | 66 KB     | ########## | 100% 
perl-sub-name-0.21   | 13 KB     | ########## | 100% 
perl-apache-test-1.4 | 115 KB    | ########## | 100% 
perl-package-depreca | 10 KB     | ########## | 100% 
muscle-3.8.1551      | 280 KB    | ########## | 100% 
perl-devel-overloadi | 8 KB      | ########## | 100% 
perl-devel-stacktrac | 16 KB     | ########## | 100% 
blast-2.9.0          | 17.7 MB   | ########## | 100% 
perl-sub-install-0.9 | 10 KB     | ########## | 100% 
perl-yaml-1.29       | 41 KB     | ########## | 100% 
perl-moo-2.003004    | 38 KB     | ########## | 100% 
ncurses-6.1          | 1.3 MB    | ########## | 100% 
perl-params-util-1.0 | 14 KB     | ########## | 100% 
perl-role-tiny-2.000 | 15 KB     | ########## | 100% 
mcl-14.137           | 2.2 MB    | ########## | 100% 
perl-package-stash-x | 21 KB     | ########## | 100% 
perl-dist-checkconfl | 10 KB     | ########## | 100% 
perl-eval-closure-0. | 11 KB     | ########## | 100% 
libssh2-1.8.2        | 257 KB    | ########## | 100% 
metagene_annotator-1 | 729 KB    | ########## | 100% 
curl-7.69.1          | 137 KB    | ########## | 100% 
perl-sub-exporter-pr | 8 KB      | ########## | 100% 
perl-file-which-1.23 | 12 KB     | ########## | 100% 
perl-devel-globaldes | 7 KB      | ########## | 100% 
krb5-1.17.1          | 1.5 MB    | ########## | 100% 
perl-class-load-0.25 | 12 KB     | ########## | 100% 
perl-module-runtime- | 7 KB      | ########## | 100% 
virsorter-1.0.5      | 47 KB     | ########## | 100% 
perl-bioperl-1.6.924 | 2.2 MB    | ########## | 100% 
perl-class-load-xs-0 | 13 KB     | ########## | 100% 
perl-module-runtime- | 15 KB     | ########## | 100% 
perl-sub-quote-2.006 | 18 KB     | ########## | 100% 
diamond-0.9.14       | 556 KB    | ########## | 100% 
perl-sub-exporter-0. | 30 KB     | ########## | 100% 
perl-parallel-forkma | 21 KB     | ########## | 100% 
perl-sub-identify-0. | 12 KB     | ########## | 100% 
openssl-1.1.1f       | 2.1 MB    | ########## | 100% 
perl-data-optlist-0. | 10 KB     | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
ERROR conda.core.link:_execute(699): An error occurred while installing package 'conda-forge::perl-5.26.2-h516909a_1006'.
Rolling back transaction: ...working... done

[Errno 22] Invalid argument: '/media/anri/FAE8F3E0E8F39959/PathoFact-master/.snakemake/conda/f8c49d3c/man/man3/App::Cpan.3'
()
console output for my data 
anri@anriPC:/media/anri/FAE8F3E0E8F39959/PathoFact-master$ conda activate PathoFact
(PathoFact) anri@anriPC:/media/anri/FAE8F3E0E8F39959/PathoFact-master$ snakemake -s Snakefile --use-conda --reason --cores 4 -p
Building DAG of jobs...
Creating conda environment envs/Biopython.yaml...
Downloading remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /media/anri/FAE8F3E0E8F39959/PathoFact-master/rules/Universal/../../envs/Biopython.yaml:
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... failed

CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/data/boston_house_prices.csv'
specified in the package manifest cannot be found.

CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/data/breast_cancer.csv'
specified in the package manifest cannot be found.

CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/data/iris.csv'
specified in the package manifest cannot be found.

CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/data/linnerud_exercise.csv'
specified in the package manifest cannot be found.

CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/data/linnerud_physiological.csv'
specified in the package manifest cannot be found.

CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/data/wine_data.csv'
specified in the package manifest cannot be found.

CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/descr/boston_house_prices.rst'
specified in the package manifest cannot be found.

CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/descr/breast_cancer.rst'
specified in the package manifest cannot be found.

CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/descr/california_housing.rst'
specified in the package manifest cannot be found.

CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/descr/covtype.rst'
specified in the package manifest cannot be found.

CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/descr/diabetes.rst'
specified in the package manifest cannot be found.

CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/descr/digits.rst'
specified in the package manifest cannot be found.

CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/descr/iris.rst'
specified in the package manifest cannot be found.

CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/descr/kddcup99.rst'
specified in the package manifest cannot be found.

CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/descr/lfw.rst'
specified in the package manifest cannot be found.

CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/descr/linnerud.rst'
specified in the package manifest cannot be found.

CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/descr/olivetti_faces.rst'
specified in the package manifest cannot be found.

CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/descr/rcv1.rst'
specified in the package manifest cannot be found.

CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/descr/twenty_newsgroups.rst'
specified in the package manifest cannot be found.

CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/descr/wine_data.rst'
specified in the package manifest cannot be found.

CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/images/china.jpg'
specified in the package manifest cannot be found.

CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/datasets/images/flower.jpg'
specified in the package manifest cannot be found.

SafetyError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/neighbors/ball_tree.cpython-36m-x86_64-linux-gnu.so'
has an incorrect size.
  reported size: 538712 bytes
  actual size: 241152 bytes

CondaVerificationError: The package for scikit-learn located at /home/anri/anaconda3/pkgs/scikit-learn-0.21.3-py36hcdab131_0
appears to be corrupted. The path 'lib/python3.6/site-packages/sklearn/utils/sparsefuncs_fast.cpython-36m-x86_64-linux-gnu.so'
specified in the package manifest cannot be found.

Whats wrong?