Hi,
I tried to download the OrgDB object provided by fungidb through annotationhub. Somehow it failed. See the commands and error below. However, downloading GRanges objects working perfectly fine. Can anyone throw some light on why OrgDB failed ?
library("AnnotationHub")
hub <- AnnotationHub()
> hub
AnnotationHub with 46259 records
# snapshotDate(): 2019-05-02
# $dataprovider: BroadInstitute, Ensembl, UCSC, ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/, Haemcode, FungiDB, Inparanoid8, TriTrypDB, PlasmoDB, AmoebaDB
# $species: Homo sapiens, Mus musculus, Drosophila melanogaster, Bos taurus, Rattus norvegicus, Pan troglodytes, Danio rerio, Gallus gallus, Mono...
# $rdataclass: GRanges, BigWigFile, TwoBitFile, OrgDb, Rle, ChainFile, EnsDb, Inparanoid8Db, TxDb, data.frame
# additional mcols(): taxonomyid, genome, description, coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
# rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH5012"]]'
title
AH5012 | Chromosome Band
AH5013 | STS Markers
AH5014 | FISH Clones
AH5015 | Recomb Rate
AH5016 | ENCODE Pilot
... ...
AH73812 | org.Plasmodium_vivax.eg.sqlite
AH73813 | org.Burkholderia_mallei_ATCC_23344.eg.sqlite
AH73814 | org.Bacillus_cereus_(strain_ATCC_14579_|_DSM_31).eg.sqlite
AH73815 | org.Bacillus_cereus_ATCC_14579.eg.sqlite
AH73816 | org.Schizosaccharomyces_cryophilus_OY26.eg.sqlite
hub_subset <- query(hub , c("fungidb" ,"OrgDb"))
> hub_subset
AnnotationHub with 277 records
# snapshotDate(): 2019-05-02
# $dataprovider: FungiDB
# $species: Naganishia albida, Albugo candida 2VRR, Albugo laibachii Nc14, Allomyces macrogynus ATCC 38327, Aphanomyces astaci, Aphanomyces invad...
# $rdataclass: OrgDb
# additional mcols(): taxonomyid, genome, description, coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
# rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH71411"]]'
title
AH71411 | Transcript information for Albugo candida 2VRR
AH71412 | Transcript information for Albugo laibachii Nc14
AH71413 | Transcript information for Allomyces macrogynus ATCC 38327
AH71414 | Transcript information for Aspergillus aculeatus ATCC 16872
AH71415 | Transcript information for Aspergillus brasiliensis CBS 101740
... ...
AH71937 | Transcript information for Phytophthora sojae P6497
AH71938 | Transcript information for Pythium vexans DAOM BR484
AH71939 | Transcript information for Saccharomyces cerevisiae S288c
AH71940 | Transcript information for Scedosporium apiospermum IHEM 14462
AH71941 | Transcript information for Yarrowia lipolytica CLIB89 W29
> hub_subset[["AH71940"]]
downloading 1 resources
retrieving 1 resource
Downloading: 240 B
Error: failed to load resource
name: AH71940
title: Transcript information for Scedosporium apiospermum IHEM 14462
reason: 1 resources failed to download
In addition: Warning messages:
1: download failed
web resource path: ‘https://annotationhub.bioconductor.org/fetch/78686’
local file path: ‘/Users/chirag/Library/Caches/AnnotationHub/25d6f57295d_78686’
reason: Forbidden (HTTP 403).
2: bfcadd() failed; resource removed
rid: BFC16
fpath: ‘https://annotationhub.bioconductor.org/fetch/78686’
reason: download failed
3: download failed
hub path: ‘https://annotationhub.bioconductor.org/fetch/78686’
cache resource: ‘AH71940 : 78686’
reason: bfcadd() failed; see warnings()
> hub_subset[["AH71412"]]
downloading 1 resources
retrieving 1 resource
Downloading: 240 B
Error: failed to load resource
name: AH71412
title: Transcript information for Albugo laibachii Nc14
reason: 1 resources failed to download
In addition: Warning messages:
1: download failed
web resource path: ‘https://annotationhub.bioconductor.org/fetch/78158’
local file path: ‘/Users/chirag/Library/Caches/AnnotationHub/25d435cd1c6_78158’
reason: Forbidden (HTTP 403).
2: bfcadd() failed; resource removed
rid: BFC17
fpath: ‘https://annotationhub.bioconductor.org/fetch/78158’
reason: download failed
3: download failed
hub path: ‘https://annotationhub.bioconductor.org/fetch/78158’
cache resource: ‘AH71412 : 78158’
reason: bfcadd() failed; see warnings()
Thanks for coming back. Waiting for your reply.
Hi @Shepherl,
I wonder if you get any updates from author.
Thanks.
Yes and I am working with them on the solution. There was a naming mismatch with the files and we are working on the re-upload
Thanks ! looking forward to it
While we are waiting for the reupload - where you interested in any other AH ids besides the two above? I might be able to implement a temporary work around while the rest of the files are being processed?
The two above should now be downloadable - I made some manually changes while we wait for the datasets to be reloaded - if you need any more please let me know
I am interested in all fungus data by fungi data (OrgDB and GRanges objects). I can wait till upload finish.
Thanks a lot. Cheers