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Bioconductor / AnnotationForge

Tools for building SQLite-based annotation data packages
https://bioconductor.org/packages/AnnotationForge
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Error when running makeOrgPackage (unable to Populate gene_info table) #39

Closed C2051 closed 1 year ago

C2051 commented 1 year ago 
    This is my command:

makeOrgPackage(gene_info=gene_info, go=gene2go, ko=koterms, pathway=gene2pathway, version="0.0.1", maintainer='wangdan 1114678784@qq.com', author='wangdan 1114678784@qq.com',outputDir="./output", tax_id="13055", genus="Chamaenerion", species="angustifolium",goTable="go") And I got this error: Populating genes table: genes table filled Populating gene_info table: Error: NOT NULL constraint failed: gene_info.GENENAME And here are the files I used. I don't know why did this happened. I would very thank you if you can help me to solve this problem.

head(gene2pathway) GID Pathway 1 evm.model.Chr1.1 ko03420 2 evm.model.Chr1.1 ko03430 3 evm.model.Chr1.1 ko03400 4 evm.model.Chr1.2 ko00910 5 evm.model.Chr1.2 ko00250 6 evm.model.Chr1.2 ko00220 head(gene_info) GID GENENAME 1 evm.model.Chr1.1 EKX90894.1 2 evm.model.Chr1.2 AGA29415.1 3 evm.model.Chr1.3 XP_004235208.1 4 evm.model.Chr1.4 KHG14627.1 5 evm.model.Chr1.5 XP_011626953.1 6 evm.model.Chr1.6 XP_008646117.1 head(gene2go) GID GO EVIDENCE 1 evm.model.Chr1.1 GO:0003677 EVA 2 evm.model.Chr1.1 GO:0003678 EVA 3 evm.model.Chr1.1 GO:0005524 EVA 4 evm.model.Chr1.1 GO:0016787 EVA 5 evm.model.Chr1.2 GO:0006520 EVA 6 evm.model.Chr1.2 GO:0016491 EVA head(koterms) GID KO 1 evm.model.Chr1.1 K03657 2 evm.model.Chr1.2 K00261 3 evm.model.Chr1.6 K00759 4 evm.model.Chr1.7 K22534 5 evm.model.Chr1.9 K13783 6 evm.model.Chr1.11 K01051

jmacdon commented 1 year ago

We have a support site at support.bioconductor.org that is more appropriate for this sort of question. In future please post this sort of question there, rather than on this GitHub repo.

The quick answer is that you have missing data in your gene_info file, in the second column. Which is what the error is telling you when it says that the NOT NULL constraint on gene_info.GENENAME is failing. In other words, there is a constraint that the GENENAME cannot be NULL (SQL term for missing), and you are failing that constraint. Filter your gene_info table and you should be fine.

C2051 commented 1 year ago

Thank you very much indeed！