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byuphamerator / phamerator-dev

Phamerator development repo
GNU General Public License v2.0
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error inserting phage genome into phage table #26

Open abdo3a opened 7 years ago

abdo3a commented 7 years ago

i have something like: error inserting phage genome into phage table There was an error adding phage somephage.gb.fixed to the database.

even after i import "db_schema.sql" and i use "fix_dnaMaster_gb.py" before importing.

do you have an idea, what the problem could be?

gregyjames commented 6 years ago

I am experianceing the same issue. No error or explaination why, just that there is a error inserting phage into database.

maculatus commented 6 years ago

Hello, I installed the program today (Head: b2b1d97d65ff9a6e8994b5bac6ddc5dd3ac60495). When I was trying to populate the database, I got this: "error inserting phage genome into phage table There was an error adding phage out64.gbk.fixed to the database. ~/Pro_ph_db/out77.gbk.fixed" It seems the same problem that greyjames and abdo3a had. Is it a way to check where the py program is failing? I can provide a genbank file for testing.

abdo3a commented 6 years ago

as @gregyjames mentioned that we don't know why some genebank doesn't insert into the database. BUT, what i did to solve this issue is: i used phamdb (https://github.com/jglamine/phamdb) to insert my phages into one DB then exported and inserted into phamerator....then Violaa working