AnnotationForge run by three days and do not end
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0
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Marcelo Laia ▴ 450
@marcelo-laia-2007
Last seen 6 months ago
Brazil

I started AnnotationForge 30, April and today I killed the R process without the end.

Before I close R, these are the output files:

marcelo@marcelo:~/Google Drive/Mlaia/egrandis/Ann_Egr$ ls -al
-rw-r--r-- 1 marcelo marcelo  2070145629 mai  1 00:49 gene2accession.gz
-rw-r--r-- 1 marcelo marcelo    23278575 mai  1 01:48 gene2go.gz
-rw-r--r-- 1 marcelo marcelo    45805597 mai  1 00:25 gene2pubmed.gz
-rw-r--r-- 1 marcelo marcelo   873197879 mai  1 01:27 gene2refseq.gz
-rw-r--r-- 1 marcelo marcelo   577669043 mai  1 01:43 gene_info.gz
-rw-r--r-- 1 marcelo marcelo  1414663752 mai  2 10:44 idmapping_selected.tab.gz
-rw-r--r-- 1 marcelo marcelo 27931828224 mai  1 01:48 NCBI.sqlite

After I run the command: kill -USR1 44587, I got these Warning messages:

Warning messages:
1: In result_fetch(res@ptr, n = n) :
  SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
2: In result_fetch(res@ptr, n = n) :
  SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
3: In result_fetch(res@ptr, n = n) :
  SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
4: In result_fetch(res@ptr, n = n) :
  SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
5: In result_fetch(res@ptr, n = n) :
  SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().

           Process R exited abnormally with code 2 at Sat May  2 10:44:34 2020

I run this command:

library(AnnotationForge)
makeOrgPackageFromNCBI(version = "0.1",
                       author = "Marcelo Laia <yyyyyyyxxxxxxxxx@gmail.com>",
                       maintainer = "Marcelo Laia <yyyyyyyxxxxxxxxx@gmail.com>",
                       outputDir = ".",
                       tax_id = "71139",
                       genus = "Eucalyptus",
                       species = "grandis")

I will restart it again. But, this run time is normal? Or I need to do extra commands?

Thank you so much!

Laia ML

sessionInfo()

I restarted R and loaded the annotationForge packages again.

R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux bullseye/sid

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=pt_BR.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=pt_BR.UTF-8        LC_COLLATE=pt_BR.UTF-8
 [5] LC_MONETARY=pt_BR.UTF-8    LC_MESSAGES=pt_BR.UTF-8
 [7] LC_PAPER=pt_BR.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
 [11] LC_MEASUREMENT=pt_BR.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
 [1] AnnotationForge_1.28.0 AnnotationDbi_1.48.0   IRanges_2.20.2
 [4] S4Vectors_0.24.4       Biobase_2.46.0         BiocGenerics_0.32.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.6   XML_3.99-0.3   digest_0.6.25  bitops_1.0-6   DBI_1.1.0 
 [6] RSQLite_2.2.0  rlang_0.4.5    blob_1.2.1     vctrs_0.2.4    bit64_0.9-7
 [11] RCurl_1.98-1.2 bit_1.1-15.2   compiler_3.6.3 memoise_1.1.0 
>
annotation AnnotationForge • 248 views
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This command should take minutes but not hours or days.

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It seems to hang at the GO data preparation stage:

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
extracting data for our organism from : gene_info
getting data for gene2go.gz
rebuilding the cache
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

I will wait to see if it finishes here.

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Marcelo Laia ▴ 450
@marcelo-laia-2007
Last seen 6 months ago
Brazil

I solved the issue. First, I downloaded the files gene2pubmed.gz, gene2accession.gz, gene2refseq.gz, gene_info.gz, gene2go.gz from ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ by wget. So, I set the rebuildCache argument to FALSE. With this, the org.Egrandis.eg.db package was created in seconds. Thanks to Kevin Blighe for your attention to help me.

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