dgront
commented
1 month ago This question can be translated into: "how many people use the original nn_make script?"
From my perspective, users typically used to get fragments from Robetta server, or from the newer version of frag_picker. If this is the case, I'd argue to downgrade the nr DB.
Please also notice, that make_fragments.pl script calls secondary structure predictors (PsiPred, Juffo, etc) which also run blast. You'd have to ensure this still work after the upgrade.
Best, Dominik Gront
sob., 13 lip 2024 o 21:57 Noora Azadvari @.***> napisał(a):
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 https://www.biostars.org/p/436501/, 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.
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There is a version incompatibility between the nr library and the BLAST version that causes the following error when running
make_fragments.pl:That's because the default nr library is upgraded to V5, but fastacmd can only read V4. There are two options here:
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.