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mouliere-lab / ITSFASTR

A bioinformatic pipeline for ultra-fast analysis of cfDNA using Oxford Nanopore Technologies sequencing.
MIT License
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¿conda? conflict with new instances of ITSFASTR #2

Open egenomics opened 2 months ago

egenomics commented 2 months ago

Hi, After some testing I am trying to download another instance of ITSFASTR so I can analyze real data. However, when I execute the code after having modified the samplesheet.csv and the config.yaml I obtain the following error in the first part of the pipeline:

Are there some incompatibility issues? Is this related with the latest changes in the repository?

(base) jlvillanueva@HCP14035:/playground/2024_cfdna_tollagu/scripts/ITSFASTR/workflow/rules/1_preprocessing$ conda activate snakemake
(snakemake) jlvillanueva@HCP14035:/playground/2024_cfdna_tollagu/scripts/ITSFASTR/workflow/rules/1_preprocessing$ snakemake --printshellcmds \
          --keep-going \
          --use-conda \
          --cores 8 \
          -s trimming.smk
/playground/2024_cfdna_tollagu/scripts/ITSFASTR/workflow/rules/1_preprocessing/trimming.smk:132: SyntaxWarning: invalid escape sequence '\;'
/playground/2024_cfdna_tollagu/scripts/ITSFASTR/workflow/rules/1_preprocessing/trimming.smk:158: SyntaxWarning: invalid escape sequence '\;'
localrules directive specifies rules that are not present in the Snakefile:
    all_trim_ONT
    all_trim_Illumina

Assuming unrestricted shared filesystem usage.
Building DAG of jobs...
Creating conda environment /playground/2024_cfdna_tollagu/scripts/ITSFASTR/workflow/rules/1_preprocessing/../../envs/preprocessing_env.yaml...
Downloading and installing remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /playground/2024_cfdna_tollagu/scripts/ITSFASTR/workflow/rules/1_preprocessing/../../envs/preprocessing_env.yaml:
Command:
mamba env create --quiet --no-default-packages --file "/playground/2024_cfdna_tollagu/scripts/ITSFASTR/workflow/rules/1_preprocessing/.snakemake/conda/b8cb13f118d51128d7d7599fd752b976_.yaml" --prefix "/playground/2024_cfdna_tollagu/scripts/ITSFASTR/workflow/rules/1_preprocessing/.snakemake/conda/b8cb13f118d51128d7d7599fd752b976_"
Output:
Channels:
 - conda-forge
 - bioconda
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... failed

CondaVerificationError: The package for bioconductor-genomeinfodb located at /home/jlvillanueva/miniforge-pypy3/pkgs/bioconductor-genomeinfodb-1.30.1-r41hdfd78af_0
appears to be corrupted. The path 'lib/R/library/GenomeInfoDb/DESCRIPTION'
specified in the package manifest cannot be found.

CondaVerificationError: The package for bioconductor-genomeinfodb located at /home/jlvillanueva/miniforge-pypy3/pkgs/bioconductor-genomeinfodb-1.30.1-r41hdfd78af_0
appears to be corrupted. The path 'lib/R/library/GenomeInfoDb/INDEX'
specified in the package manifest cannot be found.

CondaVerificationError: The package for bioconductor-genomeinfodb located at /home/jlvillanueva/miniforge-pypy3/pkgs/bioconductor-genomeinfodb-1.30.1-r41hdfd78af_0
appears to be corrupted. The path 'lib/R/library/GenomeInfoDb/NAMESPACE'
specified in the package manifest cannot be found.

CondaVerificationError: The package for bioconductor-genomeinfodb located at /home/jlvillanueva/miniforge-pypy3/pkgs/bioconductor-genomeinfodb-1.30.1-r41hdfd78af_0
appears to be corrupted. The path 'lib/R/library/GenomeInfoDb/NEWS'
specified in the package manifest cannot be found.

CondaVerificationError: The package for bioconductor-genomeinfodb located at /home/jlvillanueva/miniforge-pypy3/pkgs/bioconductor-genomeinfodb-1.30.1-r41hdfd78af_0
appears to be corrupted. The path 'lib/R/library/GenomeInfoDb/R/GenomeInfoDb'
specified in the package manifest cannot be found.

CondaVerificationError: The package for bioconductor-genomeinfodb located at /home/jlvillanueva/miniforge-pypy3/pkgs/bioconductor-genomeinfodb-1.30.1-r41hdfd78af_0
appears to be corrupted. The path 'lib/R/library/GenomeInfoDb/R/GenomeInfoDb.rdb'
specified in the package manifest cannot be found.

CondaVerificationError: The package for bioconductor-genomeinfodb located at /home/jlvillanueva/miniforge-pypy3/pkgs/bioconductor-genomeinfodb-1.30.1-r41hdfd78af_0
appears to be corrupted. The path 'lib/R/library/GenomeInfoDb/doc/Accept-organism-for-GenomeInfoDb.R'
specified in the package manifest cannot be found.

CondaVerificationError: The package for bioconductor-genomeinfodb located at /home/jlvillanueva/miniforge-pypy3/pkgs/bioconductor-genomeinfodb-1.30.1-r41hdfd78af_0
appears to be corrupted. The path 'lib/R/library/GenomeInfoDb/doc/Accept-organism-for-GenomeInfoDb.Rnw'
specified in the package manifest cannot be found.

CondaVerificationError: The package for bioconductor-genomeinfodb located at /home/jlvillanueva/miniforge-pypy3/pkgs/bioconductor-genomeinfodb-1.30.1-r41hdfd78af_0
appears to be corrupted. The path 'lib/R/library/GenomeInfoDb/doc/Accept-organism-for-GenomeInfoDb.pdf'
specified in the package manifest cannot be found.

CondaVerificationError: The package for bioconductor-genomeinfodb located at /home/jlvillanueva/miniforge-pypy3/pkgs/bioconductor-genomeinfodb-1.30.1-r41hdfd78af_0
appears to be corrupted. The path 'lib/R/library/GenomeInfoDb/doc/GenomeInfoDb.R'
specified in the package manifest cannot be found.

CondaVerificationError: The package for bioconductor-genomeinfodb located at /home/jlvillanueva/miniforge-pypy3/pkgs/bioconductor-genomeinfodb-1.30.1-r41hdfd78af_0
appears to be corrupted. The path 'lib/R/library/GenomeInfoDb/doc/GenomeInfoDb.Rnw'
specified in the package manifest cannot be found.

CondaVerificationError: The package for bioconductor-genomeinfodb located at /home/jlvillanueva/miniforge-pypy3/pkgs/bioconductor-genomeinfodb-1.30.1-r41hdfd78af_0
appears to be corrupted. The path 'lib/R/library/GenomeInfoDb/doc/GenomeInfoDb.pdf'
specified in the package manifest cannot be found.

CondaVerificationError: The package for bioconductor-genomeinfodb located at /home/jlvillanueva/miniforge-pypy3/pkgs/bioconductor-genomeinfodb-1.30.1-r41hdfd78af_0
appears to be corrupted. The path 'lib/R/library/GenomeInfoDb/doc/index.html'
specified in the package manifest cannot be found.

SafetyError: The package for bioconductor-genomeinfodb located at /home/jlvillanueva/miniforge-pypy3/pkgs/bioconductor-genomeinfodb-1.30.1-r41hdfd78af_0
appears to be corrupted. The path 'lib/R/library/GenomeInfoDb/extdata/assembly_accessions.rda'
has an incorrect size.
  reported size: 3652897 bytes
  actual size: 606208 bytes

CondaVerificationError: The package for bioconductor-genomeinfodb located at /home/jlvillanueva/miniforge-pypy3/pkgs/bioconductor-genomeinfodb-1.30.1-r41hdfd78af_0
appears to be corrupted. The path 'lib/R/library/GenomeInfoDb/extdata/dataFiles/Arabidopsis_thaliana.txt'
specified in the package manifest cannot be found.

CondaVerificationError: The package for bioconductor-genomeinfodb located at /home/jlvillanueva/miniforge-pypy3/pkgs/bioconductor-genomeinfodb-1.30.1-r41hdfd78af_0
appears to be corrupted. The path 'lib/R/library/GenomeInfoDb/extdata/dataFiles/Caenorhabditis_elegans.txt'
specified in the package manifest cannot be found.

CondaVerificationError: The package for bioconductor-genomeinfodb located at /home/jlvillanueva/miniforge-pypy3/pkgs/bioconductor-genomeinfodb-1.30.1-r41hdfd78af_0
appears to be corrupted. The path 'lib/R/library/GenomeInfoDb/extdata/dataFiles/Canis_familiaris.txt'
specified in the package manifest cannot be found.

CondaVerificationError: The package for bioconductor-genomeinfodb located at /home/jlvillanueva/miniforge-pypy3/pkgs/bioconductor-genomeinfodb-1.30.1-r41hdfd78af_0
appears to be corrupted. The path 'lib/R/library/GenomeInfoDb/extdata/dataFiles/Cyanidioschyzon_merolae.txt'
specified in the package manifest cannot be found.

CondaVerificationError: The package for bioconductor-genomeinfodb located at /home/jlvillanueva/miniforge-pypy3/pkgs/bioconductor-genomeinfodb-1.30.1-r41hdfd78af_0
appears to be corrupted. The path 'lib/R/library/GenomeInfoDb/extdata/dataFiles/Drosophila_melanogaster.txt'
specified in the package manifest cannot be found.

CondaVerificationError: The package for bioconductor-genomeinfodb located at /home/jlvillanueva/miniforge-pypy3/pkgs/bioconductor-genomeinfodb-1.30.1-r41hdfd78af_0
appears to be corrupted. The path 'lib/R/library/GenomeInfoDb/extdata/dataFiles/Homo_sapiens.txt'
specified in the package manifest cannot be found.

CondaVerificationError: The package for bioconductor-genomeinfodb located at /home/jlvillanueva/miniforge-pypy3/pkgs/bioconductor-genomeinfodb-1.30.1-r41hdfd78af_0
appears to be corrupted. The path 'lib/R/library/GenomeInfoDb/extdata/dataFiles/Mus_musculus.txt'
specified in the package manifest cannot be found.

CondaVerificationError: The package for bioconductor-genomeinfodb located at /home/jlvillanueva/miniforge-pypy3/pkgs/bioconductor-genomeinfodb-1.30.1-r41hdfd78af_0
appears to be corrupted. The path 'lib/R/library/GenomeInfoDb/extdata/dataFiles/Oryza_sativa.txt'
specified in the package manifest cannot be found.

CondaVerificationError: The package for bioconductor-genomeinfodb located at /home/jlvillanueva/miniforge-pypy3/pkgs/bioconductor-genomeinfodb-1.30.1-r41hdfd78af_0
appears to be corrupted. The path 'lib/R/library/GenomeInfoDb/extdata/dataFiles/Populus_trichocarpa.txt'
specified in the package manifest cannot be found.

CondaVerificationError: The package for bioconductor-genomeinfodb located at /home/jlvillanueva/miniforge-pypy3/pkgs/bioconductor-genomeinfodb-1.30.1-r41hdfd78af_0
appears to be corrupted. The path 'lib/R/library/GenomeInfoDb/extdata/dataFiles/Rattus_norvegicus.txt'
specified in the package manifest cannot be found.

CondaVerificationError: The package for bioconductor-genomeinfodb located at /home/jlvillanueva/miniforge-pypy3/pkgs/bioconductor-genomeinfodb-1.30.1-r41hdfd78af_0
appears to be corrupted. The path 'lib/R/library/GenomeInfoDb/extdata/dataFiles/Saccharomyces_cerevisiae.txt'
specified in the package manifest cannot be found.

CondaVerificationError: The package for bioconductor-genomeinfodb located at /home/jlvillanueva/miniforge-pypy3/pkgs/bioconductor-genomeinfodb-1.30.1-r41hdfd78af_0
appears to be corrupted. The path 'lib/R/library/GenomeInfoDb/extdata/dataFiles/Zea_mays.txt'
specified in the package manifest cannot be found.

[... MANY MORE PACKAGES ... ]
moldovannorbert commented 2 months ago

@egenomics Hm... this one is curious... The preprocessing_env.yaml is affected here, but that was modified more than a year ago, so if you could build it before you should be able to build it again. There are many corrupted path messages in your error, to me this usually means that there is something wrong with the filesystem I'm trying to write to. Can you make sure your drive space is not full, or the drive you are writing to is not failing? Or maybe something went wrong with the conda instance?