Importing bigWigs from GEO: Error in .local(con, format, text, ...) : UCSC library operation failed
#62
Comments
|
Hi @bschilder, I tried to replicate it on Linux and I think it should behave similarly on macOS. > gr <- rtracklayer::import.bw(con = URL, which = query_granges)
#R: TCP non-blocking connect() to ftp.ncbi.nlm.nih.gov timed-out in select() after 10000 milliseconds - Cancelling!: Operation #now in progress
#Error in .local(con, format, text, ...) : UCSC library operation failed
#In addition: Warning message:
#In .local(con, format, text, ...) :
# Can't get data socket for ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5684nnn/GSM5684359/suppl/GSM5684359_H3K27me3_CUTnTag_10k_HCT116_S6.hg38.rmdup.win100.bwRequest to the URL is timed out as FTP protocol has a limit is 10000 milliseconds in UCSC kent library upon which rtracklayer relies. Hence the error states the UCSC operation failed. Solution : It should work if you update the protocol to suppressPackageStartupMessages(library(rtracklayer))
URL <- "http://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5684nnn/GSM5684359/suppl/GSM5684359_H3K27me3_CUTnTag_10k_HCT116_S6.hg38.rmdup.win100.bw"
query_granges <- GenomicRanges::GRanges("chr6:165169213-167169213")
gr <- rtracklayer::import(con = URL, which = query_granges)
gr <- rtracklayer::import.bw(con = URL, which = query_granges)It's surprising to know |
|
Aha, the "http://" prefix did the trick! Never realized you could do that. Here's the outputs from my original reprex. Apologies for not thinking to include these earlier.
I'll go ahead and add a conditional to my functions that makes sure all ftp URLs have the "http://" prefix. Would it make sense to add this feature internally to Thank you so much for the quick reply and solution. All the best, |
The only way we get information about the protocol is from the prefix of the URI. Hence, the burden of providing the correct prefix is on the user. Without knowing the correct protocol, we don't know how to communicate with the resource such that we cannot operate on them. An error occurred in the screenshot because the protocol is not present in the URL. Hope this helps. |
|
In the original example I gave, the ftp:// prefix was included and gave the same error as without it. So I don't think the error my in my most recent example was exclusively due to the omission of the ftp:// prefix (though it may very well have contributed). However, now (as of April 10th 2022) I'm noticing that including the ftp:// prefix (without replacing it with http://) works when it didn't before. Has something changed with |
Nothing's changed. It is at the same commit. https://git.bioconductor.org/packages/rtracklayer
Was it the same FTP URL or some other URL?
At this moment, I'm not sure. |
Hello,
rtracklayerhas been great for importing various supplementary files from GEO. However, I've run into the following error when trying to import certain bigWig files.A couple of notes:
Reprex
GEO page.
Comes from dataset GSE188512 in a study led by @dbart1807
Error
Session info
Many thanks in advance,
Brian
The text was updated successfully, but these errors were encountered: