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silasysh 12-22-2014 03:54 AM

Blast2go pipeline
dear all,

I have two questions about blast2go.

1. Is the blast2go pipeline(b2g4pipe) still free to use. Because I checked the website of Blast2Go. The command line version need to buy. Are there any free software likw Blast2Go and it is free?

2. I still have the version 2.5 of b2g4pipe. Today, I tried to run it again. I found I can not connect to database b2g_aug12 anymore, the error message is the following:

Problem connecting to database b2g_aug12 on as blast2go with password starts with bla*****: Syntax error or access violation, message from server: "Access denied for user 'blast2go'@'%' to database 'b2g_aug12'"
Database or network connection (timeout) error for:
Annotation of 0 seqs with 0 annots finished. Now searching for orfan IPRs...
B2G-Pipe finished

Could somebody gives me a suggestion?

Thank you.


maubp 12-22-2014 09:06 AM

The good news is that b2g4pipe v2.5 is still freely available at

This was working fine for me with automated testing for my Galaxy Blast2GO (for pipelines) wrapper against the older b2g_jun11 database until a few weeks ago. In the short term I disabled the test, but have not had time to investigate if a more recent database is still available to this older version of Blast2GO:

Note that I did see network/connection failures from time to time - so you should retest your system, perhaps at different times of day to try and connect at a low usage time (e.g. very early morning in Spain, late night in USA).

However, it is clear that from v3 onwards BioBam Bioinformatics will be charging for the command line tool. It is possible they might stop supporting v2.x before too long, and given most people use their public database this would force upgrades. Wait and see?

silasysh 12-23-2014 03:59 AM

Thank you for your reply. At least the package v2.5 is still free. I found the current database becomes b2g_sep13. Now everything is okay.


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