To avoid this, you an request the file to be in the orignal format --origfmt. In cases were you cannot run the SRA toolkit or any other programs to download the file, you can still use the inbuilt commands of Linux such as wget and curl.
The standard web link for downloading the SRA files is:. If you have a large list of ids, you can simply loop it over using a while loop. Aspera uses high-speed file transfer to rapidly transfer large files and data sets over an existing WAN infrastructure. The reason this is never optimized might be that downloading from SRA is not a task you'll have to do repeatedly, as described here in this post. Not so much difference for real time though about a second.
Sign up to join this community. The best answers are voted up and rise to the top. Stack Overflow for Teams — Collaborate and share knowledge with a private group. Create a free Team What is Teams? Learn more. How do you download stuff from NCBI fast? Asked 2 years, 7 months ago.
Active 2 years, 6 months ago. I get a strange error: T prefetch. Yep, that's the whole output I get, sorry. OK, so I tried the same file again just now, and it works fine, it seems OK, thanks - how many do you reckon is the upper limit for number of prefetches?
The new tool sounds promising! But do you think this could in principle be the reason for the problem? The prefetch command is: prefetch --force no --transport http --max-size G SRR We are reviewing the output now, thank you. I'm currently hitting the same issue, stdout outputs the same as the prefetch error message above, but in my stderr logs I also see: T prefetch. I met this error too. Hi, I use the latest 2.
I have followed the thread above kwrodarmer but I dont seem to find an answer to the error below, kindly assist T prefetch. Try our latest 2. I am using 2. But for the remaining data, the error is err: file not found while copying file - cannot download 'SRR' using requested transport Please help if someone can resolve the issue. I am using sratoolkit. Thank you in advance.
We had some problems with components in the backend over the weekend. Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment.
Linked pull requests. You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. This is my download script:! The prefetch command is: prefetch --force no --transport http --max-size G SRR stdout: T prefetch. Is there a recommendation to debug this? B prefetch. Alternatively, prefetch can be used for only downloading the. C wget not recommended. Download error. Extracting fastq files from SRA files, for paired-end reads.
Converting SRA files into a single fastq file. To use in a pipe. Filter read length of SRA samples.
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