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Old 06-23-2016, 01:32 PM   #1
cascoamarillo
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Location: MA

Join Date: Oct 2010
Posts: 160
Default REPET denovo BLASTER step

Hi,
I am troubleshooting the software REPET https://urgi.versailles.inra.fr/Tools/REPET , and I got to the step 2 of TEdenovo.py analysis:

In
Code:
TEdenovo.py -P DmelChr4 -C TEdenovo.cfg -S 2 -s Blaster
the python script start to work, give you an output folder (DmelChr4_Blaster, with two additional config files), then python is no longer called and it never finish from this terminal output:

Code:
START TEdenovo.py (2016-06-23 17:21:44)
version 2.5
project name = DmelChr4
project directory = /users/work/DmelChr4_TEdenovo
beginning of step 2
self-alignment with Blaster
The copy option is: True
Anyone working with it before and having similar issues. Thanks

Last edited by cascoamarillo; 06-24-2016 at 06:45 AM.
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Old 07-07-2016, 03:33 PM   #2
mcsimenc
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Default

Hi, I had exactly the same problem. When I went into the mysql database manually and deleted the tables TEdenovo.py had created (named 'jobs' and 'info_tables' I think) then ran step 2 again it got farther. The mysql query I used was

DROP TABLE jobs;
DROP TABLE info_tables;
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Old 07-08-2016, 02:33 PM   #3
cascoamarillo
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Thank you!
OK, now stuck on step 3.....
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