addcrispraiscores - crisprverse not working
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jimjacob08 • 0
@38f51659
Last seen 1 hour ago
The Netherlands

I have been following the tutorial available online (https://github.com/crisprVerse/Tutorials/tree/master/Design_CRISPRi).

I reached the final step to evaluate the aiscores. The code stops with an error.

Code should be placed in three backticks as shown below

# include your problematic code here with any corresponding output 

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")


BiocManager::install("crisprBwa")

gs <- addSpacerAlignments(gs,
                          aligner="bowtie",
                          aligner_index=index_path,
                          bsgenome=BSgenome.Hsapiens.UCSC.hg38,
                          n_mismatches=2,
                          tssObject=tss_human,
                          tss_window=c(-500, 2000))

fastaPath <- "/Users/jimjacob/Desktop/PhD/CRISPRVERSE/hg38.fa"

mnasePath <- "/Users/jimjacob/Desktop/PhD/CRISPRVERSE/crispria_mnase_human_K562_hg38.bigWig"
dnasePath <- "/Users/jimjacob/Desktop/PhD/CRISPRVERSE/crispria_dnase_human_K562_hg38.bigWig"
fairePath <- "//Users/jimjacob/Desktop/PhD/CRISPRVERSE/crispria_faire_human_K562_hg38.bigWig"
chromatinFiles <- c(mnase=mnasePath,
                    dnase=dnasePath,
                    faire=fairePath)

results <- addCrispraiScores(gs,
                             gr=target_region,
                             tssObject=tss_human,
                             geneCol="gene_id",
                             modality="CRISPRi",
                             fastaFile=fastaPath,
                             chromatinFiles=chromatinFiles)


# please also include the results of running the following in an R session 

snapshotDate(): 2023-10-24
see ?crisprScoreData and browseVignettes('crisprScoreData') for documentation
loading from cache
+ /Users/jimjacob/Library/Caches/org.R-project.R/R/basilisk/1.14.3/0/bin/conda 'create' '--yes' '--prefix' '/Users/jimjacob/Library/Caches/org.R-project.R/R/basilisk/1.14.3/crisprScore/1.6.0/crisprai_basilisk' 'python=2.7.18' '--quiet' '-c' 'main' '-c' 'anaconda' '-c' 'bioconda' '-c' 'conda-forge'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed

PackagesNotFoundError: The following packages are not available from current channels:

  - python=2.7.18

Current channels:

  - https://conda.anaconda.org/main/osx-arm64
  - https://conda.anaconda.org/main/noarch
  - https://conda.anaconda.org/anaconda/osx-arm64
  - https://conda.anaconda.org/anaconda/noarch
  - https://conda.anaconda.org/bioconda/osx-arm64
  - https://conda.anaconda.org/bioconda/noarch
  - https://conda.anaconda.org/conda-forge/osx-arm64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://repo.anaconda.com/pkgs/main/osx-arm64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/osx-arm64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.


Error: Error creating conda environment '/Users/jimjacob/Library/Caches/org.R-project.R/R/basilisk/1.14.3/crisprScore/1.6.0/crisprai_basilisk' [exit code 1]

sessionInfo( )
R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.3

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/Amsterdam
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] crisprScoreData_1.6.0             ExperimentHub_2.10.0             
 [3] AnnotationHub_3.10.0              BiocFileCache_2.10.1             
 [5] dbplyr_2.4.0                      Rbwa_1.6.0                       
 [7] Rbowtie_1.42.0                    BSgenome.Hsapiens.UCSC.hg38_1.4.5
 [9] BSgenome_1.70.1                   rtracklayer_1.62.0               
[11] BiocIO_1.12.0                     Biostrings_2.70.2                
[13] XVector_0.42.0                    GenomicRanges_1.54.1             
[15] GenomeInfoDb_1.38.5               IRanges_2.36.0                   
[17] S4Vectors_0.40.2                  BiocGenerics_0.48.1              
[19] crisprDesignData_0.99.28          crisprDesign_1.4.0               
[21] crisprBase_1.6.0                 

loaded via a namespace (and not attached):
  [1] rstudioapi_0.15.0             jsonlite_1.8.8               
  [3] magrittr_2.0.3                GenomicFeatures_1.54.2       
  [5] fs_1.6.3                      zlibbioc_1.48.0              
  [7] vctrs_0.6.5                   memoise_2.0.1                
  [9] Rsamtools_2.18.0              RCurl_1.98-1.14              
 [11] htmltools_0.5.7               S4Arrays_1.2.0               
 [13] usethis_2.2.2                 progress_1.2.3               
 [15] curl_5.2.0                    SparseArray_1.2.3            
 [17] htmlwidgets_1.6.4             basilisk_1.14.3              
 [19] desc_1.4.3                    cachem_1.0.8                 
 [21] GenomicAlignments_1.38.2      mime_0.12                    
 [23] lifecycle_1.0.4               pkgconfig_2.0.3              
 [25] Matrix_1.6-5                  R6_2.5.1                     
 [27] fastmap_1.1.1                 GenomeInfoDbData_1.2.11      
 [29] MatrixGenerics_1.14.0         shiny_1.8.0                  
 [31] digest_0.6.34                 AnnotationDbi_1.64.1         
 [33] ps_1.7.6                      pkgload_1.3.4                
 [35] RSQLite_2.3.5                 filelock_1.0.3               
 [37] randomForest_4.7-1.1          fansi_1.0.6                  
 [39] httr_1.4.7                    abind_1.4-5                  
 [41] compiler_4.3.2                remotes_2.4.2.1              
 [43] withr_3.0.0                   bit64_4.0.5                  
 [45] BiocParallel_1.36.0           DBI_1.2.0                    
 [47] pkgbuild_1.4.3                biomaRt_2.58.1               
 [49] rappdirs_0.3.3                DelayedArray_0.28.0          
 [51] sessioninfo_1.2.2             rjson_0.2.21                 
 [53] tools_4.3.2                   interactiveDisplayBase_1.40.0
 [55] httpuv_1.6.14                 crisprScore_1.6.0            
 [57] glue_1.7.0                    restfulr_0.0.15              
 [59] callr_3.7.3                   promises_1.2.1               
 [61] grid_4.3.2                    generics_0.1.3               
 [63] tzdb_0.4.0                    hms_1.1.3                    
 [65] xml2_1.3.6                    utf8_1.2.4                   
 [67] BiocVersion_3.18.1            pillar_1.9.0                 
 [69] stringr_1.5.1                 vroom_1.6.5                  
 [71] later_1.3.2                   dplyr_1.1.4                  
 [73] lattice_0.22-5                bit_4.0.5                    
 [75] crisprBowtie_1.6.0            tidyselect_1.2.0             
 [77] miniUI_0.1.1.1                crisprBwa_1.6.0              
 [79] SummarizedExperiment_1.32.0   Biobase_2.62.0               
 [81] devtools_2.4.5                matrixStats_1.2.0            
 [83] stringi_1.8.3                 yaml_2.3.8                   
 [85] codetools_0.2-19              tibble_3.2.1                 
 [87] BiocManager_1.30.22           cli_3.6.2                    
 [89] xtable_1.8-4                  reticulate_1.35.0            
 [91] processx_3.8.3                Rcpp_1.0.12                  
 [93] dir.expiry_1.10.0             png_0.1-8                    
 [95] XML_3.99-0.16.1               parallel_4.3.2               
 [97] ellipsis_0.3.2                readr_2.1.5                  
 [99] blob_1.2.4                    basilisk.utils_1.14.1        
[101] prettyunits_1.2.0             profvis_0.3.8                
[103] urlchecker_1.0.1              bitops_1.0-7                 
[105] VariantAnnotation_1.48.1      purrr_1.0.2                  
[107] crayon_1.5.2                  rlang_1.1.3                  
[109] KEGGREST_1.42.0
crisprDesign • 76 views
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