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Clinical-Genomics / scout

VCF visualization interface
https://clinical-genomics.github.io/scout
BSD 3-Clause "New" or "Revised" License
152 stars 46 forks source link

MIssing cases #4827

Closed sofievonlanthen closed 2 months ago

sofievonlanthen commented 2 months ago

Missing cases from the last few days that were visible the other day.

Same for other users in cust004 and also cust002.

Older cases are still there. Example of missing case: 024701400228

NicoleCMMS commented 2 months ago

Same for cust003. Case 23312 was apparently rerun and uploaded to Scout on Monday but I cannot find the case at all.

northwestwitch commented 2 months ago

Oh no, we'll investigate and re-upload them, sorry for this!

northwestwitch commented 2 months ago

I just spoke with my colleagues in production and apparently we had a samples mixup problem, so they removed all the suspicious cases from scout until all was sorted. They are re-uploading the correct data as we speak (write actually).

Sorry for delay and the confusion!

sofievonlanthen commented 2 months ago

Great thanks. Did you solve the sample mixup?

dnil commented 2 months ago

Emails regarding this should have gone out to all the persons ordering - please check in with production support to get a summary of exactly this has affected your runs!

NicoleCMMS commented 2 months ago

And the case magically reappeared in Scout :-) Thanks guys!

northwestwitch commented 2 months ago

Great thanks. Did you solve the sample mixup?

Yes, all is solved. Apologies again 🙏🏻

sofievonlanthen commented 2 months ago

mine hasn't reappeared yet, but guessing it's on its way..

northwestwitch commented 2 months ago

mine hasn't reappeared yet, but guessing it's on its way..

Should be!

sofievonlanthen commented 2 months ago

our cases are still not back?

northwestwitch commented 2 months ago

our cases are still not back?

They're working on it. You should be getting a notification soon!

northwestwitch commented 2 months ago

We've just been notified that all removed cases are re-uploaded now

dnil commented 2 months ago

Ok, with that we are closing this issue. Please either contact the CG Solna support directly if you are still missing anything, or worst case just write back here and we will try to catch them! There are already three deviations open regarding the samples affected by a bug in the sequencing LIMS - and the ones taken offline while it was unclear which samples were affected (https://github.com/Clinical-Genomics/Deviations/issues/697, https://github.com/Clinical-Genomics/Deviations/issues/693, https://github.com/Clinical-Genomics/Deviations/issues/694), and I hope you have all got all the information regarding them from production you should have - otherwise please just inquire again. All the best!