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Chromosome doesn't show up/load - simple solution?

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Tanya Berardini

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Sep 5, 2023, 5:45:20 PM9/5/23
to apollo
Hi all,

We've run into a problem with our A. thaliana set up. When we started we configured with the five nuclear chromosomes, their sequences (brand new!) and tracks related to them. We had separate files for the mitochondrial (M) and chloroplast (C) genomes (sequences relatively old but very good quality) that we wanted to add as well but were so focused on the nuclear genome that we left them for later.

Now we want to add in those M and C and are running into issues. The viewer shows them as choices in the chromosome dropdown but not in the list of Ref Sequences.

M and C in dropdown.png
M and C not in Ref Sequences.png

When one tries to select either M or C, we get this error:

Error message.png

We think we've got the files in the right places but there seems to be something (simple?) that we are missing. 

Can anyone help?

Thanks very much,

Tanya

Tanya Berardini
The Arabidopsis Information Resource (TAIR)

Colin

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Sep 6, 2023, 2:19:34 PM9/6/23
to Tanya Berardini, apollo
I have not worked with Apollo in awhile but you may have to manually go into the database to insert the new reference sequences. the code lines for this are here on github

you can see here, there is a line that says "if the sequences for the organism are not loaded yet, then run the loadRefSeqs code"
 ed
and here is the loadRefSeqs code

so there is a database entry for the chromosomes/refseqs that gets initialized at startup, but if you later update the on disk file, it wouldn't get mirrored by the database, and in that case, you can manually edit the database or just restart from some amount of scratch (create a new organism directory may work, or total scratch if it gets messy)

hope that helps, I don't have the exact SQL commands you can use but I hope that 'codewise reverse engineering' helps clarify the behavior you are seeing

-Colin

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Tanya Berardini

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Sep 6, 2023, 5:56:20 PM9/6/23
to Colin, apollo
Hi Colin,

Thank you so much for your reply!  We will try this and I'll report back on the results.

Best,

Tanya

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