RosettaCommons / RosettaCommons/rosetta
BLAST version in fragmentation tools for ab initio
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- Dominant language
- C++
- Stars
- 470
- Forks
- 169
- Avg merge
- 16d 23h
- Merged PRs (30d)
- 2
Description
There is a version incompatibility between the nr library and the BLAST version that causes the following error when running make_fragments.pl:
[fastacmd] ERROR: ERROR: Cannot initialize readdb for nr database
That's because the default nr library is upgraded to V5, but fastacmd can only read V4.
There are two options here:
- Downgrading nr library
- Upgrading BLAST
The new BLAST is faster, but it needs more work and rewriting of code. Downgrading nr is an easier fix.
I want to know your opinion, before working on it, should we downgrade nr or upgrade BLAST? And of course, I would appreciate any help in fixing this.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with make_fragments.pl and reproduce the fastacmd error using the nr library version described in the issue. Review how the script invokes fastacmd and determine whether the supported path is a library downgrade or a BLAST upgrade; done means fragmentation runs without the nr database initialization error.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100