Question

Error MakeOrgPackagefromNCBI

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cinzia.spagnoli • 0

@dfb033f2

Last seen 16 days ago

Finland

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

Bioconductor • 349 views

ADD COMMENT • link updated 16 days ago by James W. MacDonald 64k • written 9 weeks ago by cinzia.spagnoli • 0

James W. MacDonald · Answer 1 · 2023-10-03

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James W. MacDonald 64k

@james-w-macdonald-5106

Last seen 1 day ago

United States

You will rarely find a particular strain in any annotation data, and instead you should use the 'main' taxon ID, which for A. baumannii happens to be 470.

## how many genes for 470?
$ awk '$1 == 470' gene_info | wc -l
3733
## now how about 575584
$ awk '$1 == 575584' gene_info | wc -l
0

No idea how many genes one might expect for this bacterium, but you will get better results using 470.

ADD COMMENT • link 9 weeks ago James W. MacDonald 64k

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I tried, but it does not seem to work.

> library(AnnotationForge)
> makeOrgPackageFromNCBI(version = "0.1",
+                          author = "Cinzia Spagnoli cinzia.spagnoli@uniroma3.it",
+                          maintainer = "Cinzia Spagnoli cinzia.spagnoli@uniroma3.it",
+                          outputDir = ".",
+                          tax_id = "470",
+                          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
rebuilding the cache
extracting data for our organism from : gene2pubmed
getting data for gene2accession.gz
rebuilding the cache
extracting data for our organism from : gene2accession
getting data for gene2refseq.gz
rebuilding the cache
extracting data for our organism from : gene2refseq
getting data for gene_info.gz
rebuilding the cache
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  error reading from the connection
In addition: Warning messages:
1: In .Internal(shortRowNames(x, type)) :
  closing unused connection 3 (D:/OneDrive - Universita degli Studi Roma Tre/Documenti/gene2pubmed.gz)
2: call dbDisconnect() when finished working with a connection 
3: In scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  :
  invalid or incomplete compressed data

ADD REPLY • link updated 9 weeks ago by James W. MacDonald 64k • written 9 weeks ago by cinzia.spagnoli • 0

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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.

> makeOrgPackageFromNCBI("0.0.1","me <me@mine.org>","me", tax_id = "470", genus = "Acinetobacter", species = "baumannii", rebuildCache = FALSE)
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
processing alias data
processing refseq data
processing accession data
processing GO data
making the OrgDb package ...
Populating genes table:
genes table filled
Populating pubmed table:
pubmed table filled
Populating gene_info table:
gene_info table filled
Populating entrez_genes table:
entrez_genes table filled
Populating alias table:
alias table filled
Populating refseq table:
refseq table filled
Populating accessions table:
accessions table filled
Populating go table:
go table filled
table metadata filled

'select()' returned many:1
mapping between keys and columns
Dropping GO IDs that are too new for the current GO.db
Populating go table:
go table filled
Populating go_bp table:
go_bp table filled
Populating go_cc table:
go_cc table filled
Populating go_mf table:
go_mf table filled
'select()' returned many:1
mapping between keys and columns
Populating go_bp_all table:
go_bp_all table filled
Populating go_cc_all table:
go_cc_all table filled
Populating go_mf_all table:
go_mf_all table filled
Populating go_all table:
go_all table filled
Creating package in c:/Users/jmacdon/Desktop/org.Abaumannii.eg.db 
Now deleting temporary database file
complete!
[1] "org.Abaumannii.eg.sqlite"

> install.packages("org.Abaumannii.eg.db", type = "source", repos = NULL)
Installing package into 'C:/Users/jmacdon/AppData/Local/R/win-library/4.3'
(as 'lib' is unspecified)
* installing *source* package 'org.Abaumannii.eg.db' ...
<snip>
* DONE (org.Abaumannii.eg.db)
> library(org.Abaumannii.eg.db)

> select(org.Abaumannii.eg.db, head(keys(org.Abaumannii.eg.db)), "SYMBOL")
'select()' returned 1:1 mapping
between keys and columns
       GID        SYMBOL
1 66395337          dnaA
2 66395338          dnaN
3 66395339          recF
4 66395340          gyrB
5 66395341          cybC
6 66395342 F3P16_RS00030

> sessionInfo()
R version 4.3.0 (2023-04-21 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22621)

ADD REPLY • link 9 weeks ago James W. MacDonald 64k

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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/

ADD REPLY • link 17 days ago cinzia.spagnoli • 0

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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?).

ADD REPLY • link 16 days ago James W. MacDonald 64k