Issue in downloading SRA data using SRA tool kit

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1

Hi all,

I am currently downloading SRA data using SRA tool kit with prefetch and fastq-dump commands. However, I have an issue to get some clarifications.
When I use prefetch -v SRR********, in first situation, it gives me the following results;

File_1
File_11526×168 8.19 KB

In second situation, it gives me the following results;

File_2
File_21523×189 8.66 KB

In second situation, I had 'SRR***** has 0 unresolved dependencies'

However, I was able to have FASTQ files downloaded in both situations in my directory while the data downloading is much faster in second situation. It would be very helpful for me to know whether there is any issue of the downloading complete data in the second situation where 'SRR***** has 0 unreolved dependencies' is indicated. Or else, is it okay for me to proceed with the data downloading regardless of those differences? I really appreciate your comments for my problem!
Thanks in advance!

2

Hi @mneranjan31

It looks like you are trying to download amplicon data generated from a microbiota survey. You may want to checkout and install the new QIIME 2 plugin q2-fondue.

-Mike

2 Likes
3

Hi Mike,

Thank you for the useful information!!!. I will check the q2-fondue plugin for the data download. BTW, could you make sure whether the way I did [prefetch and fastq-dump] would be possible to download data and proceed with QIIME2 analysis or not applicable? Thanks you once again!

Madhawa