ericscript.pl --downdb fail :: wrong generated url

[Eric Deveaud]

FYI


while ensemble ftp server provides the following

ftp://ftp.ensembl.org/pub/release-84/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.toplevel.fa.gz


running ericscript.pl  --downdb --refid mus_musculus fail with the following error message:


[EricScript] Downloading mus_musculus data. This process may take from few minutes to few hours depending on the selected genome ...Error in download.file(file.path("ftp://ftp.ensembl.org/pub", paste("release-",  :
  cannot open URL 'ftp://ftp.ensembl.org/pub/release-84/fasta/mus_musculus/dna/Mus_musculus.GRCm38.73.dna.toplevel.fa.gz'
Execution halted
done.

same with --ensversion happens

I did not investigated the lib/R/DownloadDB.R scripts to see where the

running Version: 0.5.5a  (https://sourceforge.net/projects/ericscript/files/ericscript-0.5.5.tar.bz2)

regards

Eric

[Matteo Benelli]

Hi Eric,

thanks for your feedback. it seems that you have a not up-to-date (or wrong) version of the RefID.RData file (under lib/data/_resources).. RefID.RData is automatically created and updated each time you access to the ensembl ftp.. Have you some problems accessing to the ensembl ftp? 

Try to remove RefID.RData and re-rerun ericscript.

ps: I will release the ready-to-use db data for mus musculus asap and update ericscript package by cleaning those files.

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[Eric Deveaud]

thanks for the fast answer.

I try rigth now and let you know

bests

Eric

[Eric Deveaud]

same problem.

bic-soft:ericscript/ericscript-0.5.5 > rm lib/data/_resources/RefID.RData
bic-soft:ericscript/ericscript-0.5.5 > perl ericscript.pl  --downdb --refid mus_musculus             

[EricScript] Downloading mus_musculus data. This process may take from few minutes to few hours depending on the selected genome ...Error in download.file(file.path("ftp://ftp.ensembl.org/pub", paste("release-",  :
  cannot open URL 'ftp://ftp.ensembl.org/pub/release-84/fasta/mus_musculus/dna/Mus_musculus.GRCm38.73.dna.toplevel.fa.gz'
Execution halted

looking at the lib/R/DownloadDB.R and runnig the following code snippet

I got this.

bic-soft:/ericscript/ericscript-0.5.5 > R --no-save

R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> load(file.path('/local/gensoft2/src/ericscript/ericscript-0.5.5', "lib", "data", "_resources", "RefID.RData"))
> ix.refid <- which(refid == 'mus_musculus')
> ix.refid
[1] 34
> refid.path
 [1] "Ailuropoda_melanoleuca.ailMel1.73.dna.toplevel.fa.gz"   
 [2] "Anas_platyrhynchos.BGI_duck_1.0.73.dna.toplevel.fa.gz"  
 [3] "Anolis_carolinensis.AnoCar2.0.73.dna.toplevel.fa.gz"    
 [4] "Bos_taurus.UMD3.1.73.dna.toplevel.fa.gz"                
 [5] "Caenorhabditis_elegans.WBcel235.73.dna.toplevel.fa.gz"  
 [6] "Callithrix_jacchus.C_jacchus3.2.1.73.dna.toplevel.fa.gz"
 [7] "Canis_familiaris.CanFam3.1.73.dna.toplevel.fa.gz"       
 [8] "Cavia_porcellus.cavPor3.73.dna.toplevel.fa.gz"          
 [9] "Choloepus_hoffmanni.choHof1.73.dna.toplevel.fa.gz"
 [9] "Choloepus_hoffmanni.choHof1.73.dna.toplevel.fa.gz"      
[10] "Ciona_intestinalis.KH.73.dna.toplevel.fa.gz"            
[11] "Ciona_savignyi.CSAV2.0.73.dna.toplevel.fa.gz"           
[12] "Danio_rerio.Zv9.73.dna.toplevel.fa.gz"                  
[13] "Dasypus_novemcinctus.dasNov2.73.dna.toplevel.fa.gz"     
[14] "Dipodomys_ordii.dipOrd1.73.dna.toplevel.fa.gz"          
[15] "Drosophila_melanogaster.BDGP5.73.dna.toplevel.fa.gz"    
[16] "Echinops_telfairi.TENREC.73.dna.toplevel.fa.gz"         
[17] "Equus_caballus.EquCab2.73.dna.toplevel.fa.gz"           
[18] "Erinaceus_europaeus.HEDGEHOG.73.dna.toplevel.fa.gz"     
[19] "Felis_catus.Felis_catus_6.2.73.dna.toplevel.fa.gz"      
[20] "Ficedula_albicollis.FicAlb_1.4.73.dna.toplevel.fa.gz"   
[21] "Gadus_morhua.gadMor1.73.dna.toplevel.fa.gz"             
[22] "Gallus_gallus.Galgal4.73.dna.toplevel.fa.gz"            
[23] "Gasterosteus_aculeatus.BROADS1.73.dna.toplevel.fa.gz"   
[24] "Gorilla_gorilla.gorGor3.1.73.dna.toplevel.fa.gz"        
[25] "Homo_sapiens.GRCh37.73.dna.toplevel.fa.gz"              
[26] "Ictidomys_tridecemlineatus.spetri2.73.dna.toplevel.fa.gz"
[27] "Latimeria_chalumnae.LatCha1.73.dna.toplevel.fa.gz"      
[28] "Loxodonta_africana.loxAfr3.73.dna.toplevel.fa.gz"       
[29] "Macaca_mulatta.MMUL_1.73.dna.toplevel.fa.gz"            
[30] "Macropus_eugenii.Meug_1.0.73.dna.toplevel.fa.gz"        
[31] "Meleagris_gallopavo.UMD2.73.dna.toplevel.fa.gz"         
[32] "Microcebus_murinus.micMur1.73.dna.toplevel.fa.gz"       
[33] "Monodelphis_domestica.BROADO5.73.dna.toplevel.fa.gz"    
[34] "Mus_musculus.GRCm38.73.dna.toplevel.fa.gz"              
[35] "Mustela_putorius_furo.MusPutFur1.0.73.dna.toplevel.fa.gz"
[36] "Myotis_lucifugus.Myoluc2.0.73.dna.toplevel.fa.gz"       
[37] "Nomascus_leucogenys.Nleu1.0.73.dna.toplevel.fa.gz"      
[38] "Ochotona_princeps.pika.73.dna.toplevel.fa.gz"           
[39] "Oreochromis_niloticus.Orenil1.0.73.dna.toplevel.fa.gz"  
[40] "Ornithorhynchus_anatinus.OANA5.73.dna.toplevel.fa.gz"   
[41] "Oryctolagus_cuniculus.OryCun2.0.73.dna.toplevel.fa.gz"  
[42] "Oryzias_latipes.MEDAKA1.73.dna.toplevel.fa.gz"          
[43] "Otolemur_garnettii.OtoGar3.73.dna.toplevel.fa.gz"       
[44] "Pan_troglodytes.CHIMP2.1.4.73.dna.toplevel.fa.gz"       
[45] "Pelodiscus_sinensis.PelSin_1.0.73.dna.toplevel.fa.gz"   
[46] "Petromyzon_marinus.Pmarinus_7.0.73.dna.toplevel.fa.gz"  
[47] "Pongo_abelii.PPYG2.73.dna.toplevel.fa.gz"               
[48] "Procavia_capensis.proCap1.73.dna.toplevel.fa.gz"        
[49] "Pteropus_vampyrus.pteVam1.73.dna.toplevel.fa.gz"        
[50] "Rattus_norvegicus.Rnor_5.0.73.dna.toplevel.fa.gz"       
[51] "Saccharomyces_cerevisiae.EF4.73.dna.toplevel.fa.gz"     
[52] "Sarcophilus_harrisii.DEVIL7.0.73.dna.toplevel.fa.gz"    
[53] "Sorex_araneus.COMMON_SHREW1.73.dna.toplevel.fa.gz"      
[54] "Sus_scrofa.Sscrofa10.2.73.dna.toplevel.fa.gz"           
[55] "Taeniopygia_guttata.taeGut3.2.4.73.dna.toplevel.fa.gz"  
[56] "Takifugu_rubripes.FUGU4.73.dna.toplevel.fa.gz"          
[57] "Tarsius_syrichta.tarSyr1.73.dna.toplevel.fa.gz"         
[58] "Tetraodon_nigroviridis.TETRAODON8.73.dna.toplevel.fa.gz"
[59] "Tupaia_belangeri.TREESHREW.73.dna.toplevel.fa.gz"       
[60] "Tursiops_truncatus.turTru1.73.dna.toplevel.fa.gz"       
[61] "Vicugna_pacos.vicPac1.73.dna.toplevel.fa.gz"            
[62] "Xenopus_tropicalis.JGI_4.2.73.dna.toplevel.fa.gz"       
[63] "Xiphophorus_maculatus.Xipmac4.4.2.73.dna.toplevel.fa.gz"


all the refid.path contains the problematic 73.

still looking in the code in order to find where it is set like that.

regards

Eric

[Matteo Benelli]

Please try to download again ericscript (0.5.5b) and rerun the code.

[Eric Deveaud]

Le mardi 3 mai 2016 19:07:02 UTC+2, matteobenelli a écrit :

Please try to download again ericscript (0.5.5b) and rerun the code.

yep, this solved the problem.

thanks

Eric

[mary...@genomezoo.net]

What is the link for 0.5.5b?