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I need to create an orgDb for my microorganism, but it gives me an error that I'll report below:
> > makeOrgPackageFromNCBI(version = "0.1",
> + author = "Cinzia Spagnoli cinzia.spagnoli@uniroma3.it",
> + maintainer = "Cinzia Spagnoli cinzia.spagnoli@uniroma3.it",
> + outputDir = ".",
> + tax_id = "575584",
> + genus = "Acinetobacter",
> + species = "baumannii")
> If files are not cached locally this may take awhile to assemble a 33
> GB cache databse in the NCBIFilesDir directory. Subsequent calls to this function should be faster (seconds). The cache will try to rebuild once per day.Please also see AnnotationHub for some pre-builtOrgDb downloads preparing data from NCBI ...
> starting download for
> [1] gene2pubmed.gz
> [2] gene2accession.gz
> [3] gene2refseq.gz
> [4] gene_info.gz
> [5] gene2go.gz
> getting data for gene2pubmed.gz
> extracting data for our organism from : gene2pubmed getting data for
> gene2accession.gz extracting data for our organism from :
> gene2accession getting data for gene2refseq.gz extracting data for our
> organism from : gene2refseq getting data for gene_info.gz extracting
> data for our organism from : gene_info getting data for gene2go.gz
> extracting data for our organism from : gene2go processing gene2pubmed
> processing gene_info: chromosomes processing gene_info: description
> Error in prepareDataFromNCBI(tax_id, NCBIFilesDir, outputDir, rebuildCache, :
> no information found for species with tax id 575584
I tried, but it does not seem to work.
It might be due to either the spaces in your path, or the fact that it's a OneDrive directory. It's normally better to just use the Desktop and delete after installing.
I apologize for the delay in responding. However, the command still doesn't work for me. I would need to create the package from this genome: https://www.ncbi.nlm.nih.gov/nuccore/NZ_CP058289.1/
I don't know what to tell you. I already told you that you can't build it for that strain, and you have to use 470 instead. I can get it to build (see above), and told you not to use a OneDrive path. Saying 'the command still doesn't work for me' without code or output isn't helpful at all (doesn't work how?).
Hello, while working on different projects, I recently got back to working on this code. I tried running your code again, but it's not working, even though I manually downloaded these files into the working directory: [1] gene2pubmed.gz [2] gene2accession.gz [3] gene2refseq.gz [4] gene_info.gz [5] gene2go.gz
Here the code:
That error indicates that you already have a file called NCBI.sqlite in your working directory, and it's incomplete (missing the gene2accession_date table). Here's mine:
The easiest thing to do is to delete your NCBI.sqlite DB and then run
makeOrgDbFromNCBIagain. But do note that you have to add rebuildCache = FALSE to your call, or you will download all those files again!Well, thanks for the advice! i resubmitted the program and this is what I get. Fortunately, it downloaded most of the .gz files for me, but it crashed at GO.
Two remarks:
You can increase the time out further to (for example) 4000 seconds through
options(timeout = 4000).Although not related to the time out, note that you did not correctly follow the naming convention for specifying the author and maintainer; the mail should be between
<and>. See?makeOrgPackageFromNCBI, that tells you to do that like this:I did it! After several attempts and your invaluable advice! Now I'm trying to perform GO and KEGG enrichment analysis. I also followed the advice given in this link: "No genes can be mapped...." using enrichGO in clusterProfiler But it does not work, can you help me?
Happy to hear you got it working!
Please open a new thread for your new question. Yet, before you do so, double-check that the object/input
GO_analysisis a character vector, and that these are indeed entrez ids (and thus match with the reportedExpected input gene IDs). In other words, first do all the checks that I suggested in my post you linked to...!