there is any chance that I can continue downloading a database which stopped in the middle?
I mean, if i have the accession info list, using that can I continue downloading from anywhere that stopped in the middle of running? or using something else or even there is a method that doing it by itself
Pls let me know how to do it.
Hi @shanif3 ,
Welcome to the forum!
Could you please clarify what command you are running?
Hi @Nicholas_Bokulich ,
Thanks for answering!
I'm downloading using qiime. I don't have a specific command.
I mean I know how to download data, but I want to add a feature which help me if the running stopped in the middle of downloading the data and then i will continue to download the data from the same point instead downloading everything again
so my question is how can i do it?
It depends which command you are running. Could you please give us more information on how you are downloading sequences with QIIME 2?
I have a git on this project: GitHub - YarinBekor/YaMAS: YaMAS is a package designed to easily download DNA datasets from the NCBI SRA website. It is developed by the YOLO lab team, and is designed to be simple, efficient, and easy to use for non-programmer users.
pls see the source code- you can find the code about downloading data in: create_visualization.py
Hi @shanif3 ,
Thanks for clarifying! This answers a few of my questions. I thought maybe you were using an existing tool in QIIME 2 for downloading databases (we have a few different tools and the answer would be different, depending on which database you want to use).
We already have a QIIME 2 plugin for downloading raw data (of any type) from NCBI SRA, which already implements a strategy for re-downloading failed accession IDs:
So I would recommend using that for downloading data, and linking it to your pipeline, as it looks like you want to pipe data into QIIME 2 in other steps of your pipeline.
Another comment on your pipeline: it looks like you use the QIIME 2 CLI in your pipeline mixed in with other python code. I would recommend using QIIME 2's Python API in this case, as it would probably be less cumbersome than mixing command-line and python when working with QIIME 2 inputs/outputs. But the QIIME 2 Python API is less well documented at the moment, so that is one good reason to ignore my comment!
There is a specific command that i can use? or i need to do all the process of downloading code again?
Hi @shanif3 ,
Yes, you can use one of the
get-* actions, like
get-all to download all accessions that you need. This function will retry a specified number of times for each dataset, until all are downloaded. It will also report which accessions failed, so you can try again later or manually inspect.
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