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PATRIC3 / patric3_website

Legacy PATRIC Website (JBoss Portal Version)
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What are Deprecated genomes? #2451

Open Sveta-user opened 8 months ago

Sveta-user commented 8 months ago

Greetings - There is a group of genomes in BV-BRC from Bioproject: PRJNA745059 that all occur in 4 copies , of which 3 are flagged "Deprecated" , while the 4th is flagged as "WGS" in this field: Genome Status (not "Sequencing Status field). They appear identical in Contig #, quality markers, size, etc. Differ only by Date Inserted I wasn't aware of this flaw and included many of these "deprecated" genomes in several Trees. The trees kind off worked, but poorly: they finished when 100 protein families were requested (Job ID: 13361103), but did not finish when 500 families were requested (Job ID: 13361107). Questions: Are Deprecated genomes safe to use? What is wrong with them (other than redundancy) ?
Could they have caused some Trees to fail ?

Would really appreciate your insight image

olsonanl commented 7 months ago

Hi - these are mostly likely identical duplicates that were loaded due to issues in the data load pipeline. @mshukla1 has started marking these as deprecated.

Sveta-user commented 7 months ago

Thank you for the clarification, Bob! Appreciate you taking the time