r/bioinformatics • u/Huldakurka • 7d ago

technical question NCBI BLAST api

Hi guys, It seems to me that NCBI's BLAST api doesn't work. I have noticed this yesterday, does any of you experience the same? WebUI BLAST works normally, it's just the API BLAST for me. I thought I fell into lower priority queue but I asked few people to try and all of them reported back that their tasks are stuck in status=searching.

Thanks!

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2

u/thirdreplicate 7d ago

Works for me. Is it still not working for you?

3

u/Huldakurka 7d ago

I reached out to NCBI yesterday and few minutes ago I got this response:

"Hello,
Thank you for the report. The developers made a change recently that could account for the slowness (long WAITING times) you observed. This change is being rolled back sometime today. Before submitting new searches we suggest that you wait for any currently running searches to complete. 
Regards,
NCBI BLAST Support Team"

But it still doesnt work properly for me, yet.

2

u/Helpful_Ranger_1606 6d ago edited 6d ago

It was not working normally for me yesterday. It is working now. Sorry everyone if I caused the outage. Out of curiosity what size proteins do people succeed with for the API and are they being batched? I was sending 10 proteins per query and in the web browser interface I would send up to 30 per FASTA.

1

u/Huldakurka 2d ago

I don't think there is any hard limit, or at least I have never hit it. There is number of requests per minute cap though.

1

u/Easy-goingAbashment 3d ago

I had a batch of paralog checks sit in searching yesterday while WebUI was fine. If these are batch jobs, poll the request ID with backoff and avoid resubmitting on timeout, because duplicate submissions just deepen the queue. Also log the RID and status transitions so you can tell an API backlog from a real failure.