Entering edit mode
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
