Git Product home page Git Product logo

Comments (4)

jmabuin avatar jmabuin commented on August 20, 2024

Can you paste here the command you used to launch SparkBWA?

from sparkbwa.

avapirev avatar avapirev commented on August 20, 2024

Here (same works with paired reads)

spark-submit --conf spark.ui.enabled=true --class com.github.sparkbwa.SparkBWA --master yarn --deploy-mode cluster --driver-memory 40G --executor-memory 20G --executor-cores 4 --num-executors 100 --verbose $EBROOTSPARKBWA/SparkBWA-0.2.jar -m -r --hdfs --index ${Index_File} -n 100 data/R1.fastq data/Output_ERR000589_sam

For completeness - paired-reads command:

spark-submit --conf spark.ui.enabled=true --class com.github.sparkbwa.SparkBWA --master yarn --deploy-mode cluster --driver-memory 40G --executor-memory 20G --executor-cores 4 --num-executors 100 --verbose $EBROOTSPARKBWA/SparkBWA-0.2.jar -m -r -p --hdfs --index ${Index_File} -n 100 data/R1.fastq data/R2.fastq data/Output_ERR000589_sam

from sparkbwa.

jmabuin avatar jmabuin commented on August 20, 2024

SparkBWA, by default, uses paired reads. To use single reads you need to specify the "-s" option. It should be something like:

spark-submit --conf spark.ui.enabled=true --class com.github.sparkbwa.SparkBWA --master yarn --deploy-mode cluster --driver-memory 40G --executor-memory 20G --executor-cores 4 --num-executors 100 --verbose $EBROOTSPARKBWA/SparkBWA-0.2.jar -m -r -s --hdfs --index ${Index_File} -n 100 data/R1.fastq data/Output_ERR000589_sam

I am going to update the documentation with all the available options. Please, let me know if this works for you.

from sparkbwa.

avapirev avatar avapirev commented on August 20, 2024

Thank you. With explicitly putting '-s' it works. I had the feeling I had done it before but maybe it was not on HDFS data.

edit: works on Spark standalone too. Thanks.

from sparkbwa.

Related Issues (20)

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.