Confirmed and pending status: Tool "Retrieve bold" is not working : warning message + log

usegalaxy.eu support
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1

Does not work, always same error:

Tool standard error :

Warning message:
In data.table::fread(text = x, header = header, sep = sep, ...) :
  Stopped early on line 44. Expected 2 fields but found 0. Consider fill=TRUE and comment.char=. First discarded non-empty line: <<ga('create', 'UA-372370-4', 'auto');>>

Log message :

researched marker(s): COI-5P 

Processing  Osmia bicornis 
Osmia bicornis marker list: 
no sequences were found with selected marker(s) for Osmia bicornis see existing marker list above

I’ve tried different species (one single or more) and I checked if it exists on BOLD and NCBI separately and it works.

I tried different formats of typing the species (eg. Osmia bicornis, “Osmia bicornis”, Osmia bicornis[tax], “Osmia bicornis”[tax]) etc

I really tried everything that I could, even putting the marker or having a header etc but always the same error message with no retrieval.

What is wrong?

Maybe because BOLD system has been off since a few days???

Systems Offline Notice:

Notice: BOLD Public Data Portal is temporarily unavailable. Other BOLD Services will continue to be functional in the meantime. Please check back later or contact support at support@boldsystems.org

Would be very grateful for any help. Have already discussed with GalaxyAI but no solution works.

2

I think the tool is outdated as far as I can see. Here the issue page of the package behind it Issues · ropensci/bold · GitHub

As a temp solution you can try to go to https://portal.boldsystems.org/api/query?query=tax:species:Osmia bicornis&extent=full in a browser, this gives you a api token. Then again in your browser go to https://portal.boldsystems.org/api/documents/<query_id>/download?format=tsv (replace <query_id> with your token) and save as tsv to get the data. Then you need to process that yourself into a fasta format. You might want to check out the tool Tabular-to-FASTA in galaxy (never used it myself).

3

Thanks @gbbio and I agree that retrieving the data directly would be one way to get around the current issues!

I’ve open a ticket against the development repository to learn more about if this is known and if there are any plans for an update.

Thanks for asking @eline.jkn !! :slight_smile:

ps: I am going to annotate this topic in a way that helps it to show up at the bottom of tool forms, to help other people who run into the same issue to find our discussion and the current status. Just please know that this is not actually “resolved” yet until the the tool is either functional or confirmed to be deprecated. Any of us here can continue the discussion while this is happening.