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WGSExtract / WGSExtract.github.io

WGS Extract WWW home
https://WGSExtract.github.io/
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Download link is broken for the hs38d1s #16

Closed 4Liberty closed 1 year ago

4Liberty commented 1 year ago

Hello, I have a bam file from https://sequencing.com. However, when I try to download their reference genome hs38d1s, WGS Extract gives an error. Therefore, I checked the source link from genomes.vcf file and I noticed that its OneDrive link is not accessible.

hs38d1s,WGSE,hs38d1s.fa.gz,hs38d1s.fa.gz, https://api.onedrive.com/v1.0/shares/s!AgorjTSMFYpjgR0QualUlHx53-0U/root/content,hs38d1s (by Sequencing),2581,Num,hs38d1s (Sequencing.com; hs38d1+22_KI270879v1_alt) (@WGSE)

screenshot2

Could someone please provide me an alternative download link for the hg38d1s? I couldn't find it anywhere on the internet. I am an amateur in this field and would appreciate any help.

RandyHarr commented 1 year ago

Thank you for doing the more thorough investigation. It does appear ALL the files with links to our MS Onedrive server are missing. Investigating now and likely have to restore from backup. CORRECTION: Only the Reference Genome files. The other links are still fine. Such that program installs still work.

On 25 May 2023 we restructured our online file stores to remove all uses of Google Drive. This was due to the continual changing of process and breaking of links that Google kept introducing with large file support; even with paid accounts. We suspect during this shuffling is when the reference directory was removed.

hs38d1s is a custom model we built because Sequencing.com decided to develop a custom model for their BAM alignment. You will not find it anywhere. We had to create it after looking at the headers of their BAM.

We will get it restored soon. Worse case, you may have to update your genomes.csv with a file we provide if we cannot restore the same links. Now that Bitly supports MS Onedrive, we may change the references to Bitly short links that we can retarget anywhere. Or simply move the file repositories to our own server.

Give me an hour to fix everything. UPDATE: Working to restore. Restoring out of the MS Onedrive trash did not restore the links. So we are trying to roll back to before the change (within MS Onedrive directly) to see if that restores the same share links. This takes a while for MS to do it seems.

RandyHarr commented 1 year ago

Rolling back to a date in MS Onedrive is not like MS Windows which unwinds the journaling file system. It is more like Google Docs where it simply creates a new version, as of that date and time, of what things looked like at that previous date. Thus updating all files and changing all their share URLs. So now everything is broken.

While we work to fix everything (installs, upgrades, etc), here is the URL for the reference genome you are looking for. See https://github.com/WGSExtract/WGSExtract.github.io/issues/17#issuecomment-1599576217 for more details.

https://get.wgse.io/hs38d1s.fa.gz

I will close the issue for now because once the system is working for everyone, it will work for you. Once working again, simply rerun the installer to get the new files with links.