Deleted:Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and annotation forge
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Manmohit ▴ 10
@7ffaf7cf
Last seen 2.2 years ago
United States

I am trying to make orgdb package for my bacteria (Pseudomonas aeruginosa PAO1) but when I am trying to run makeAnnDbPkg command it gives me error which is difficult for me as a beginner to resolve

hub <- AnnotationHub() query(hub, c("pseudomonas")) org.PAO1.eg.db <- hub[["AH91625"]] file.copy(AnnotationHub::cache(ah3["AH91625"]),"./org.Pseudomonas aeruginosa PAO1.eg.sqlite") seed <- new("AnnDbPkgSeed", Package="./org.Pseudomonas aeruginosa PAO1.eg.db", Version="0.0.1", PkgTemplate="NCBIORG.DB",AnnObjPrefix="org.Pseudomonas aeruginosa PAO1.eg",organism="Pseudomonas aeruginosa",species="Pseudomonas aeruginoa PAO1")

include your problematic code here with any corresponding output

makeAnnDbPkg(seed,"./org.Pseudomonas aeruginosa PAO1.eg.sqlite")

Error in initWithDbMetada(x, dbfile) : "metadata" table has unexpected col names

sessionInfo( ) R version 4.2.1 (2022-06-23) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Monterey 12.6

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

Random number generation: RNG: Mersenne-Twister Normal: Inversion Sample: Rounding

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

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

other attached packages: [1] shiny_1.7.3 RSQLite_2.2.19 ggplot2_3.4.0
[4] DESeq2_1.36.0 SummarizedExperiment_1.26.1 MatrixGenerics_1.8.1
[7] matrixStats_0.63.0 GenomicRanges_1.48.0 GenomeInfoDb_1.32.4
[10] MeSHDbi_1.32.0 AnnotationHub_3.4.0 BiocFileCache_2.4.0
[13] dbplyr_2.2.1 AnnotationForge_1.38.1 AnnotationDbi_1.58.0
[16] IRanges_2.30.1 S4Vectors_0.34.0 edgeR_3.38.4
[19] limma_3.52.4 NOISeq_2.40.0 Matrix_1.5-3
[22] Biobase_2.56.0 BiocGenerics_0.42.0

loaded via a namespace (and not attached): [1] bitops_1.0-7 bit64_4.0.5
[3] filelock_1.0.2 RColorBrewer_1.1-3
[5] httr_1.4.4 bslib_0.4.1
[7] tools_4.2.1 DT_0.26
[9] utf8_1.2.2 R6_2.5.1
[11] colorspace_2.0-3 DBI_1.1.3
[13] withr_2.5.0 tidyselect_1.2.0
[15] bit_4.0.5 curl_4.3.3
[17] compiler_4.2.1 cli_3.4.1
[19] DelayedArray_0.22.0 sass_0.4.4
[21] scales_1.2.1 genefilter_1.78.0
[23] rappdirs_0.3.3 digest_0.6.30
[25] rmarkdown_2.18 XVector_0.36.0
[27] pkgconfig_2.0.3 htmltools_0.5.3
[29] fastmap_1.1.0 htmlwidgets_1.5.4
[31] rlang_1.0.6 rstudioapi_0.14
[33] jquerylib_0.1.4 generics_0.1.3
[35] jsonlite_1.8.3 crosstalk_1.2.0
[37] BiocParallel_1.30.4 dplyr_1.0.10
[39] RCurl_1.98-1.9 magrittr_2.0.3
[41] GenomeInfoDbData_1.2.8 munsell_0.5.0
[43] Rcpp_1.0.9 fansi_1.0.3
[45] lifecycle_1.0.3 yaml_2.3.6
[47] zlibbioc_1.42.0 grid_4.2.1
[49] blob_1.2.3 parallel_4.2.1
[51] promises_1.2.0.1 crayon_1.5.2
[53] lattice_0.20-45 Biostrings_2.64.1
[55] annotate_1.74.0 KEGGREST_1.36.3
[57] locfit_1.5-9.6 knitr_1.41
[59] pillar_1.8.1 geneplotter_1.74.0
[61] codetools_0.2-18 XML_3.99-0.13
[63] glue_1.6.2 BiocVersion_3.15.2
[65] evaluate_0.18 BiocManager_1.30.19
[67] png_0.1-8 vctrs_0.5.1
[69] httpuv_1.6.6 gtable_0.3.1
[71] purrr_0.3.5 assertthat_0.2.1
[73] cachem_1.0.6 xfun_0.35
[75] mime_0.12 xtable_1.8-4
[77] later_1.3.0 survival_3.4-0
[79] tibble_3.1.8 memoise_2.0.1
[81] ellipsis_0.3.2 interactiveDisplayBase_1.34.0

```

AnnotationHub AnnotationForge Pseudomonas_aeruginosa • 346 views
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