The Place for Comparative Genomics
Joined November 2013
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15 Photos and videos
2 Nov 2018
Derivative data (datasets derived from primary data such as blast databases, fasta sequences for coding sequences, analysis results) take up 75TB of storage These are currently cached for about 1 month and files not used after that are deleted (don't worry, they get regenerated).
2 Nov 2018
Primary data in CoGe (DNA Sequences, variant/SNP, expression, etc.) takes up ~22TB
2 Nov 2018
Some facts about CoGe (since I needed this information):
Relational Database: Mysql
Contains over 8,000,000,000 rows
Total size 2.2TB
Only contains metadata about genomes (e.g., organism, genomic features such as genes, etc.) Has no primary sequence, variant, RNASeq, MethySeq..
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2 Nov 2018
CoGe is back up!!!
Database was updated successfully. My preliminary set of sets (load genome, load annotations, SynMap, GEvo, and CoGeBlast) all worked without any issues. Please email coge.genome@gmail.com if you run into any problems.
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2 Nov 2018
CoGe tables update completed! I'm moving the database to a dedicated partition (don't want it to fill due other system activity). Hoping to start testing in the next hour or two.
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1 Nov 2018
Last table is still updating. Also did a double check and found one more table that needed to be update . I'm hoping that tomorrow will be the day CoGe comes back. If not, I will be checking over the weekend and will work to get CoGe up as soon as possible.
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1 Nov 2018
Progress report on CoGe: 4/5 tables have been updated to BIGINT for feature_ids. One table left. I've been running these updates in parallel, so am hopeful that the final update will be finished sometime today.
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31 Oct 2018
Database backups completed. Started the table updates last night, but saw that space was going to be limiting on the partition holding the database. A copy of the database has been installed on a larger partition and is currently having the first table updated.
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30 Oct 2018
Database is currently being backed up (we do that weekly, but want to capture the latest changes since Sunday, just in case.)
30 Oct 2018
We had some additional difficulty due to using CyVerse's LDAP for authentication, which also went down (both systems have no problems for years and crash at the same time -- how do they know?)
30 Oct 2018
We have identified the problem (mysql ran out of numbers for primary keys) and need to change those to bigint.
30 Oct 2018
We received reports that CoGe was throwing errors when loading genomes.
10 Nov 2016
Hey CoGe users, please take a moment to complete our future directions survey! It'll only take a minute! goo.gl/forms/HXxdwBSqFnuX9W2…
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3 Nov 2016
CoGe User/Data associations- blue is users (size is amount of data), red shows data collections, purple is genomes, and green is experiments
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1 Nov 2016
Publication for our latest fractionation bias assessment tool ("FractBias") is now available! Read it here: goo.gl/zNfTRp
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23 Sep 2016
Voice your opinion on the future of JBrowse...take the survey tinyurl.com/h8dkpk4 @gmodproject
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