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IBEXCluster edited this page Nov 13, 2022 · 6 revisions

Welcome to Rice Variant Calling!

This demo session will be used for hands-on workshop at ISRFG '22.

Principal investigator:

Prof. Rod A. Wing, Director, Center for Desert Agriculture,4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, KSA

Developers:

Nagarajan Kathiresan {nagarajan.kathiresan@kaust.edu.sa} and Yong Zhou {yong.zhou@kaust.edu.sa}

Contact us:

For any pipeline support, suggestions and collaborations, please contact us pipeline.cda@gmail.com

Demo in Workstation or Laptop using Docker.

Prerequisite:

  1. Docker installation on your laptop/workstation.

  2. Download the demo rice genome dataset and pipeline scripts:

    Download link

  3. untar the download file:

    tar -xzvf rice_pipeline_demo.tar.gz

  4. Change to rice_pipeline_demo directory. This directory will be your working directory for this demo exercise.

    cd rice_pipeline_demo

  5. Your directory structure for demo exercise will be:

     ~/Rice_pipeline/rice_pipeline_demo$ tree -L 2
   ├── input
        ├── ERS467814_ERR614071_1.fastq.gz
        ├── ERS467814_ERR614071_2.fastq.gz
        ├── ERS467814_ERR614072_1.fastq.gz
        ├── ERS467814_ERR614072_2.fastq.gz
        ├── ERS467860_ERR615300_1.fastq.gz
        ├── ERS467860_ERR615300_2.fastq.gz
        ├── ERS467860_ERR615301_1.fastq.gz
        └── ERS467860_ERR615301_2.fastq.gz
   ├── output
   ├── ref
        ├── Nipponbare_chr.dict
        ├── Nipponbare_chr.fasta
        ├── Nipponbare_chr.fasta.amb
        ├── Nipponbare_chr.fasta.ann
        ├── Nipponbare_chr.fasta.bwt
        ├── Nipponbare_chr.fasta.fai
        ├── Nipponbare_chr.fasta.pac
        └── Nipponbare_chr.fasta.sa
  ├── scripts
        ├── Phase1
        ├── Phase2
        ├── Phase3
        └── Phase4
  └── tmp

  6. Download the docker image:

    sudo docker pull ibexcluster/biohpc:v1.0

  7. Ensure the docker image is available in your workstation/Laptop:

    sudo docker images

  8. Start the docker image and include the mount points (source $PWD and destinations /demo):

    sudo docker run -d -it --name biohpc --mount type=bind,source="$(pwd)",target=/demo ibexcluster/biohpc:v1.0

  9. Ensure the docker image is running at your workstation:

    sudo docker ps -a

Input and Reference data preparation:

We are providing 2 rice genome samples (ERS467814 and ERS467860). To improve the quality, each samples are resequenced two times and the summary is as follows (All these *.fastq.gz files are in the input directory):

   Sample #1
  ├── ERS467814_ERR614071_1.fastq.gz
  ├── ERS467814_ERR614071_2.fastq.gz
  ├── ERS467814_ERR614072_1.fastq.gz
  ├── ERS467814_ERR614072_2.fastq.gz
   Sample #2
  ├── ERS467860_ERR615300_1.fastq.gz
  ├── ERS467860_ERR615300_2.fastq.gz
  ├── ERS467860_ERR615301_1.fastq.gz
  └── ERS467860_ERR615301_2.fastq.gz

We are providing Nipponbare rice genome reference along with all the required index files and it's available in ref directory.

  ├── Nipponbare_chr.dict
  ├── Nipponbare_chr.fasta
  ├── Nipponbare_chr.fasta.amb
  ├── Nipponbare_chr.fasta.ann
  ├── Nipponbare_chr.fasta.bwt
  ├── Nipponbare_chr.fasta.fai
  ├── Nipponbare_chr.fasta.pac
  └── Nipponbare_chr.fasta.sa

Phase 1: Genome mapping

Step 1: Prepare your input files. i.e., Copy the list of unique forward sequence files from input/ directory into scripts/Phase1/Phase1.txt file directory.

cd input/

ls -lrta *_1.fastq.gz | awk '{print $9}' > ../scripts/Phase1/ Phase1.txt

Step 2: Execute the MPI wrapper program for Phase 1:

  • One core will be assigned to 1 sample (by default)
  • Number of MPI processes (-np)should be equal to the number of samples listed in the Phase1.txt file

sudo docker exec -ti biohpc sh -c "mpirun --allow-run-as-root -np 4 /demo/scripts/Phase1/Phase1.exe"

Phase 2. Variants discovery

Step 1: Prepare for Phase 2 execution.

  1. List the Sample names and update into Phase2.prefix.txt

ls -ld output/tmpBAM/* | awk -F'/' '{print $NF}' > scripts/Phase2/Phase2.prefix.txt

  1. List the sample directories and update into Phase2.directory.txt

ls -ld output/tmpBAM/* | awk '{print "/demo/"$9} ' > scripts/Phase2/Phase2.directory.txt

  1. Find the number of MPI process (-np) for multi-core runs.

cat scripts/Phase2/Phase2.prefix.txt | wc -l

(This number should be used as an argument for multi-core runs)

Step 2: Execute the MPI wrappers

sudo docker exec -ti biohpc sh -c "mpirun --allow-run-as-root -np 2 /demo/scripts/Phase2/Phase2.exe"

Phase 3. Call set refinement and combining variants

Step 1: Execute the Prerequisite data distribution script with number of Cores available in your workstation. Here I’m using 112 cores in my workstation.

sudo docker exec -ti biohpc sh -c "sh /demo/scripts/Phase3/Phase3.prerequisite.optimized.sh 112"

Step 2: Launch the MPI wrapper script for Phase 3.

sudo docker exec -ti biohpc sh -c "mpirun --allow-run-as-root --oversubscribe -np 84 /demo/scripts/Phase3/Phase3.exe"

Phase 4. Variants matrixes

Step 1: Run the Prerequisite sudo docker exec -ti biohpc sh -c " sh /demo/scripts/Phase4/Phase4.prerequisite.sh"

Step 2: Run the Variant caller program

sudo docker exec -ti biohpc sh -c "mpirun --allow-run-as-root --oversubscribe -np 12 /demo/scripts/Phase4/Phase4.exe"

Results

Successfully completed results are available here:
Phase #1: Results
Phase #2: Results
Phase #3: Results
Phase #4: Results

Contact

For your comments, feedback and support, please contact us: pipeline.cda@gmail.com

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