Error in Matches

[rafischulman]

Hi,

Thank you so much for this excellent tool. I've been using it as an efficient way to query many sequences from across a region.
Lately I've been having some trouble downloading sequences and metadata. See below for my error message.

I used one of your query examples from the readme to get a list of accession IDs, then hit the error when I attempt to download.

Thanks for the help.

#GISAID login
credentials <- login(username = "", password = "")

df <- query(

• credentials = credentials,
• location = "Oceania",
• from_subm = "2024-07-26",
• to_subm = "2024-07-28",
• fast = TRUE
• )
  Selecting all 6 accession_ids.
  Returning 0-6 of 6 accession_ids.

head(df$accession_id)
[1] "EPI_ISL_19293748" "EPI_ISL_19293749" "EPI_ISL_19293750" "EPI_ISL_19293751" "EPI_ISL_19293752" "EPI_ISL_19293753"

full_df <- download(credentials = credentials, list_of_accession_ids = df$accession_id, get_sequence=TRUE)
Selecting entries...
Error in matches[[1]][[2]] : subscript out of bounds

[PabloOfEpidemiology]

Getting the same error!

[Wytamma]

It looks like gisaid has added a capture to stop automated access. I'd suggest saving the accession_ids to a file and manually entering them into the full text search field.

[PabloOfEpidemiology]

Interestingly I usually can download a first few batches upon the first run of the script, but then around 6th batch (1 batch is only 10 sequences) the error comes out. Here's the console:
Downloading batch 1 out of 40
Selecting entries...
Compressing data. Please wait...
Data ready.
Downloading...
tar: Removing leading '/' from member names
Downloading batch 2 out of 40
Selecting entries...
Compressing data. Please wait...
Data ready.
Downloading...
tar: Removing leading '/' from member names
Downloading batch 3 out of 40
Selecting entries...
Compressing data. Please wait...
Data ready.
Downloading...
tar: Removing leading '/' from member names
Downloading batch 4 out of 40
Selecting entries...
Compressing data. Please wait...
Data ready.
Downloading...
tar: Removing leading '/' from member names
Downloading batch 5 out of 40
Selecting entries...
Compressing data. Please wait...
Data ready.
Downloading...
tar: Removing leading '/' from member names
Downloading batch 6 out of 40
Selecting entries...
Encountered an error: subscript out of bounds

Then if I rerun the script, the error happens during the very first run. So it takes time for their UI to detect automation.

[dawnmy]

It looks like gisaid has added a capture to stop automated access. I'd suggest saving the accession_ids to a file and manually entering them into the full text search field.

This really sucks