UShER error

[Keith Durkin]

Hi
I have been using UShER for the last few months for checking the placement of SARS-CoV-2 genomes we sequence in relation to existing data and it has become an invaluable tool

However lately I get the following message when I try and upload a sequence:

Warning/Error(s):
Missing usher protobuf file (config setting in hgPhyloPlaceData/hg38/config.ra = (null)

Get the same result with a sequence ID

Any help would be appreciated

Thanks

Keith

[Angie Hinrichs]

Hi Keith,

Sorry about that!  Hope to have it fixed soon.  In the meantime, please try this link:

https://genome.ucsc.edu/cgi-bin/hgPhyloPlace?db=wuhCor1

Angie

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Angie Hinrichs, Bioinformatics Programmer

UCSC Genome Browser

UC Santa Cruz Genomics Institute

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[Angie Hinrichs]

Hi Keith,

So sorry about that!  The tree, at over 12 million sequences, has crossed a file size threshold that I did not anticipate a couple years ago when writing the code, and since then I forgot about that limitation.  I hope to have that fixed soon as well.  Thanks so much for reporting the error!  

Angie

On Wed, Sep 14, 2022 at 4:09 AM Keith Durkin <keith...@gmail.com> wrote:

Hi Angie 

The link you provided worked when I tried it on the 12th, however today using the GISAID genomes option I get the following error: Why did we not get EOF starting out with BIGNUM?

It works fine with the gene bank option (I get the same result with the link this link https://genome.ucsc.edu/cgi-bin/hgPhyloPlace)

Thanks for your help 

Keith 

To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CADyET8O2tNavtrMRPkKRVSCKWmLS7Oi7KG_1mt9KGWEKL4o-8g%40mail.gmail.com.

[Keith Durkin]

Hi Angie 

The link you provided worked when I tried it on the 12th, however today using the GISAID genomes option I get the following error: Why did we not get EOF starting out with BIGNUM?

It works fine with the gene bank option (I get the same result with the link this link https://genome.ucsc.edu/cgi-bin/hgPhyloPlace)

Thanks for your help 

Keith 

On 12 Sep 2022 at 23:21:27, Angie Hinrichs <an...@soe.ucsc.edu> wrote:

To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CADyET8O2tNavtrMRPkKRVSCKWmLS7Oi7KG_1mt9KGWEKL4o-8g%40mail.gmail.com.

[Keith Durkin]

Hi Angie 

Thanks for letting me know and thanks for the tool its a great help.

All the best 

Keith 

[Angie Hinrichs]

Hi Keith,

The error is fixed now, thanks again for reporting it.  

Angie