rnaQUAST-2.1.0/BUSCO, blast-2.10.0 multithreading problem?

Question

[sunnykevin97]

HI

I performing quality checking for assembled transcripts using rnaQUAST-2.1.0 with BUSCO as an additional parameter. rnaQUAST runs smoothly with given computational power (threads 16). when It starts the BUSCO step, it runs only on 1 thread as a default, It may be because of multithreading issues in tblastn (using ncbi-blast-2.10.0+) ? If I'm not wrong, I tried with an older version of ncbi-blast-2.3.0, during the BUSCO step, it runs only on 1 thread as a default. Please let me know where I'm doing wrong.

Thanks

Answer 1

[h.mon]

Make sure you are using a recent version of BUSCO (e.g. 4.1.3), and BLAST+ 2.10.1 or later. However, you will have to check if rnaQUAST is compatible with BUSCO4 releases.

TBLASTN had a multi-theading bug until recently, it seems this has been fixed in BLAST+ 2.10.1:

BLAST+ 2.10.1: June 8, 2020
Bug fixes
Fix for TBLASTN Multi-Threading bug.

BUSCO developers noted this bug and, in old versions of BUSCO, recommended using BLAST+ 2.3 or older (however, this didn't fix the issue for me back when I first encountered it). For some BUSCO releases, the TBLASTN step was restricted to 1 thread regardless of the --threads setting, to avoid the bug.

In the latest BUSCO version (currently at 4.1.3), the developers recommend BLAST+ 2.10.1, and the thread restriction at the TBLASTN step has been lifted.

[sunnykevin97]

Just now I realized BUSCO has been updated 6 days before. Thanks for the suggestions.

[sunnykevin97]

I tried to install BUSCO v4.1.2 using conda install -c bioconda busco, it installing only the older version of BUSCO 4.0.6.

[h.mon]

Check the order of the conda channels, and install BUSCO at a new environment, not at the base environment.

[pinn]

I'm also facing the same problem with BUSCO, as @sunnykevin97 pointed out. unable to install newest version. Can you show me how do I order of the conda channels, and install BUSCO at a new environment.

[GenoMax]

To set the correct order of channels in bioconda

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

Then do

conda create -n busco busco
conda activate busco