No URLs working, I could not download the metadata database

[Majid-Soheili]

I tried to download the full version of the metadata database by using the SRAdb, but unfortunately, I didn't succeed.

timeStart <- proc.time()
sqlfile <- getSRAdbFile()
trying URL 'https://gbnci-abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz'
Error in download.file(url_sra, destfile = localfile, mode = "wb", method = method) :
cannot open URL 'https://gbnci-abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz'
proc.time() - timeStart
user system elapsed
0.02 0.00 0.68

As you can see, the URL could not be opened.
So, I tried to test other links.
url_sra <- "https://s3.amazonaws.com/starbuck1/sradb/SRAmetadb.sqlite.gz"

download.file(url_sra, destfile = "test.txt", mode = "wb", method = "auto")
trying URL 'https://s3.amazonaws.com/starbuck1/sradb/SRAmetadb.sqlite.gz'
Error in download.file(url_sra, destfile = "test.txt", mode = "wb", method = "auto") :
cannot open URL 'https://s3.amazonaws.com/starbuck1/sradb/SRAmetadb.sqlite.gz'

Any help would be appreciated.

[MPintil]

I have the exact same issue. I would appreciate if anyone could write a solution to this.
The code which I tried to run is:
sqlfile <-'SRAmetadb.sqlite'

if(!file.exists('SRAmetadb.sqlite')) sqlfile <<- getSRAdbFile()
sra_con <- dbConnect(SQLite(),sqlfile)
getSRAdbFile(destdir = getwd(),

•          destfile = "SRAmetadb.sqlite.gz",method='auto')
  

trying URL 'https://gbnci-abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz'
Error in download.file(url_sra, destfile = localfile, mode = "wb", method = method) :
cannot open URL 'https://gbnci-abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz'

The details of my R session are below:
sessionInfo()
R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8

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

other attached packages:
[1] SRAdb_1.58.0 RCurl_1.98-1.8 graph_1.74.0 RSQLite_2.2.15 GEOquery_2.64.2
[6] Biobase_2.56.0 BiocGenerics_0.42.0

loaded via a namespace (and not attached):
[1] Rcpp_1.0.9 pillar_1.8.0 compiler_4.2.1 BiocManager_1.30.18 bitops_1.0-7
[6] tools_4.2.1 bit_4.0.4 memoise_2.0.1 lifecycle_1.0.1 tibble_3.1.8
[11] pkgconfig_2.0.3 rlang_1.0.4 DBI_1.1.3 cli_3.3.0 fastmap_1.1.0
[16] dplyr_1.0.9 xml2_1.3.3 generics_0.1.3 vctrs_0.4.1 hms_1.1.1
[21] stats4_4.2.1 bit64_4.0.5 tidyselect_1.1.2 glue_1.6.2 data.table_1.14.2
[26] R6_2.5.1 fansi_1.0.3 limma_3.52.2 tidyr_1.2.0 tzdb_0.3.0
[31] readr_2.1.2 purrr_0.3.4 blob_1.2.3 magrittr_2.0.3 ellipsis_0.3.2
[36] utf8_1.2.2 cachem_1.0.6

[risserlin]

I am having the same issue with GEOmetadb that is usually found in the SRAdb directory

getSQLiteFile(destdir = getwd(), destfile = "GEOmetadb.sqlite.gz")
trying URL 'http://starbuck1.s3.amazonaws.com/sradb/GEOmetadb.sqlite.gz'
Error in download.file(url_geo, destfile = localfile, mode = "wb") :
cannot open URL 'http://starbuck1.s3.amazonaws.com/sradb/GEOmetadb.sqlite.gz'
In addition: Warning message:
In download.file(url_geo, destfile = localfile, mode = "wb") :
cannot open URL 'http://starbuck1.s3.amazonaws.com/sradb/GEOmetadb.sqlite.gz': HTTP status was '403 Forbidden’

[tobbyxy]

Having the same issues, all links seem to be broken.

[tobbyxy]

wget https://s3.amazonaws.com/starbuck1/sradb/SRAmetadb.sqlite.gz
--2022-08-18 10:29:24-- https://s3.amazonaws.com/starbuck1/sradb/SRAmetadb.sqlite.gz
Resolving s3.amazonaws.com (s3.amazonaws.com)... 52.217.73.30
Connecting to s3.amazonaws.com (s3.amazonaws.com)|52.217.73.30|:443... connected.
HTTP request sent, awaiting response... 403 Forbidden
2022-08-18 10:29:24 ERROR 403: Forbidden.

[mkempenaar]

For anyone still having this issue; the links now refer to a HTML page that contain a link to the correct file. The following command worked to download it manually:

curl -L -O https://gbnci.cancer.gov/sra/SRAmetadb.sqlite.gz

Current download is about 3.6GB and extracts to a 51GB sqlite file.