Question: error while making database using Annotationforge package
gravatar for kritikamish99
2.8 years ago by
kritikamish9910 wrote:

Hello All,

Please bear with me i have one silly question. I using clusterprofiler package for gene ontology study. Because my sample database is not present in given package so i need to make it. For making database i am using annotationforge library this is my command :

setwd(dir = "/home/Psuedo/tmp/")

makeOrgPackageFromNCBI(version="NC_002516.2",author="",maintainer= "",outputDir = ".",tax_id = "208964", genus="Pseudomonas" ,species = "Pseudomonas aeruginosa PAO1" )

it will run 3-4 hours after that it will give me error saying

Creating package in ./org.PPseudomonas aeruginosa
chmod: cannot access ‘./org.PPseudomonas’: No such file or directory
chmod: cannot access ‘aeruginosa’: No such file or directory
chmod: cannot access ‘’: No such file or directory
chmod: cannot access ‘aeruginosa’: No such file or directory
chmod: cannot access ‘’: No such file or directory
Now deleting temporary database file
[1] "org.PPseudomonas aeruginosa"
Warning message:
In .makeAnnDbPkg(x, dbfile, dest_dir = dest_dir, =,  :
  chmod 444 ./org.PPseudomonas aeruginosa aeruginosa failed

my file have permission for allthings still it giving me error

and these are my output files which are generated

gene2accession.gz           gene_info.gz
gene2pubmed.gz              NCBI.sqlite
gene2refseq.gz                 org.PPseudomonas aeruginosa

but it ends giving me error

please help me out as i need this urgently.

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

 [1] LC_CTYPE=en_IN.UTF-8       LC_NUMERIC=C               LC_TIME=en_IN.UTF-8       
 [7] LC_PAPER=en_IN.UTF-8       LC_NAME=C                  LC_ADDRESS=C              

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

other attached packages:
 [1] GO.db_3.3.0            RSQLite_1.0.0          DBI_0.4-1              httr_1.2.1            
 [5] biomaRt_2.28.0         RCurl_1.95-4.8         bitops_1.0-6           AnnotationForge_1.14.2
 [9] AnnotationDbi_1.34.4   IRanges_2.6.1          S4Vectors_0.10.2       Biobase_2.32.0        
[13] BiocGenerics_0.18.0   

loaded via a namespace (and not attached):
[1] XML_3.98-1.4       GenomeInfoDb_1.8.3 R6_2.1.2           tools_3.3.1       


ADD COMMENTlink modified 2.8 years ago by Guido Hooiveld2.4k • written 2.8 years ago by kritikamish9910
Answer: error while making database using Annotationforge package
gravatar for Guido Hooiveld
2.8 years ago by
Guido Hooiveld2.4k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.4k wrote:


I am not an expert on bacteria, and this is not really an answer to your question [though I noticed you have spaces in the species name], but please note that through the AnnotationHub infrastructure an EntrezGene-based (NCBI) annotation library is available.


> library(AnnotationHub)
> hub = AnnotationHub()
snapshotDate(): 2016-07-14
> # Query for Pseudomonas
> query(hub, c("Pseudomonas"))
AnnotationHub with 35 records
# snapshotDate(): 2016-07-14
# $dataprovider: NCBI,, Inparanoid8
# $species: Pseudomonas aeruginosa, Pseudomonas aeruginosa_PAO1, Pseudomonas...
# $rdataclass: OrgDb, Inparanoid8Db
# additional mcols(): taxonomyid, genome, description, tags, sourceurl,
#   sourcetype
# retrieve records with, e.g., 'object[["AH10565"]]'

  AH10565 | hom.Pseudomonas_aeruginosa.inp8.sqlite               
  AH12818 |            
  AH12869 |              
  AH12938 |
  AH12940 |          
  ...       ...                                                  
  AH48510 |            
  AH48516 |              
  AH48538 |
  AH48582 |              
  AH48621 |             
> # Now see that: AH48510 |
> <- hub[["AH48510"]]
> # check
> columns( annotation data can be retrieved?
 [6] "GENENAME"    "GID"         "GO"          "GOALL"       "ONTOLOGY"   
[11] "ONTOLOGYALL" "PMID"        "REFSEQ"      "SYMBOL"     
> keytypes( identifiers can be queried with?
 [6] "GENENAME"    "GID"         "GO"          "GOALL"       "ONTOLOGY"   
[11] "ONTOLOGYALL" "PMID"        "REFSEQ"      "SYMBOL"     
> select(, head(keys(, c("SYMBOL", "GENENAME", "GO"))
'select()' returned 1:many mapping between keys and columns
      GID SYMBOL                  GENENAME         GO
1  877569  pyoS5                 pyocin S5 GO:0016021
2  877569  pyoS5                 pyocin S5 GO:0019835
3  877569  pyoS5                 pyocin S5 GO:0050829
4  877570 PA1021       enoyl-CoA hydratase GO:0016853
5  877571 PA0123 transcriptional regulator GO:0003677
6  877571 PA0123 transcriptional regulator GO:0003700
7  877571 PA0123 transcriptional regulator GO:0006351
8  877572 PA0891      hypothetical protein GO:0016788
9  877572 PA0891      hypothetical protein GO:0046872
10 877573 PA1020    acyl-CoA dehydrogenase GO:0050660
11 877573 PA1020    acyl-CoA dehydrogenase GO:0016627
12 877574 PA0440            oxidoreductase GO:0005737
13 877574 PA0440            oxidoreductase GO:0051536
14 877574 PA0440            oxidoreductase GO:0016491
ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by Guido Hooiveld2.4k

Hi Guido thanks for this help

I have one more query suppose i have denovo data then in that the reference will not be available so i can't use clusterprofiler for my denovo samples. Or should i need to customise the annotationhub  specific for my sample

ADD REPLYlink written 2.8 years ago by kritikamish9910

Mmm, I am sorry but I don't understand your question...

ADD REPLYlink written 2.8 years ago by Guido Hooiveld2.4k
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