CoGe

The Place for Comparative Genomics

[CoGe @CoGeUpdates]

CoGe's downtime explained: https://t.co/E1eSjGR8r6

[CoGe @CoGeUpdates]

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).

[CoGe @CoGeUpdates]

Primary data in CoGe (DNA Sequences, variant/SNP, expression, etc.) takes up ~22TB

[CoGe @CoGeUpdates]

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..

[CoGe @CoGeUpdates]

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 [email protected] if you run into any problems.

[CoGe @CoGeUpdates]

@rm0sher Thanks Becky. While I don't want to jinks it, I think we are in the home stretch.

[CoGe @CoGeUpdates]

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.

[CoGe @CoGeUpdates]

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.

[CoGe @CoGeUpdates]

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.

[CoGe @CoGeUpdates]

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.

[CoGe @CoGeUpdates]

Backup is still running, (no problems have been reported.)

[CoGe @CoGeUpdates]

Database is currently being backed up (we do that weekly, but want to capture the latest changes since Sunday, just in case.)

[CoGe @CoGeUpdates]

@CyVerseOrg LDAP is back up and we are back on CoGe's main server.

[CoGe @CoGeUpdates]

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?)

[CoGe @CoGeUpdates]

We have identified the problem (mysql ran out of numbers for primary keys) and need to change those to bigint.

[CoGe @CoGeUpdates]

We received reports that CoGe was throwing errors when loading genomes.

[CoGe @CoGeUpdates]

CoGe is currently undergoing unscheduled maintenance.

[CoGe @CoGeUpdates]

Hey CoGe users, please take a moment to complete our future directions survey! It'll only take a minute! https://t.co/USNwUH6BQf

[CoGe @CoGeUpdates]

New Look, Same Great Tools!
Check out our new style at https://t.co/07MIsxAkNF

[CoGe @CoGeUpdates]

CoGe User/Data associations- blue is users (size is amount of data), red shows data collections, purple is genomes, and green is experiments