Question

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

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4.2 years ago

sunnykevin97 ▴ 990

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

RNA-Seq • 1.7k views

ADD COMMENT • link updated 4.2 years ago by h.mon 35k • written 4.2 years ago by sunnykevin97 ▴ 990

score 3 · Answer 1 · 2020-09-22

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4.2 years ago

h.mon 35k

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.

ADD COMMENT • link 4.2 years ago by h.mon 35k

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

ADD REPLY • link 4.2 years ago by sunnykevin97 ▴ 990

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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.

ADD REPLY • link 4.2 years ago by sunnykevin97 ▴ 990

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

ADD REPLY • link 4.2 years ago by h.mon 35k

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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.

ADD REPLY • link 4.2 years ago by pinn ▴ 210

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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

ADD REPLY • link 4.2 years ago by GenoMax 147k