Giter VIP home page Giter VIP logo

Comments (4)

nityendra21 avatar nityendra21 commented on September 19, 2024 1

That worked excellently. Thank you @kmnip

from rna-bloom.

dvirdi01 avatar dvirdi01 commented on September 19, 2024

Hi, I was having the same issue while assembling my long-read files today.

It gives me the following errors for some files:

> Stage 3: Assemble long reads for "rnabloom"
Overlapping sequences...
Parsed 10,196,100 overlap records in 16m 1s
total reads:    1,947,378
 - unique:      356,315 (18.3 %)
   - multi-seg: 48,497
Unique reads extracted in 29.242s
ERROR: Error extracting unique reads!
ERROR: Error assembling long reads!

AND this for other files

Overlapping sequences...
ERROR: Index 3 out of bounds for length 3
java.lang.ArrayIndexOutOfBoundsException: Index 3 out of bounds for length 3
        at rnabloom.io.PafRecord.update(PafRecord.java:34)
        at rnabloom.io.ExtendedPafRecord.update(ExtendedPafRecord.java:32)
        at rnabloom.io.PafReader.next(PafReader.java:63)
        at rnabloom.olc.Layout.extractUniqueFromOverlaps(Layout.java:1660)
        at rnabloom.olc.OverlapLayoutConsensus.overlapWithMinimapAndExtractUnique(OverlapLayoutConsensus.java:156)
        at rnabloom.olc.OverlapLayoutConsensus.uniqueOLC(OverlapLayoutConsensus.java:1159)
        at rnabloom.RNABloom.assembleUnclusteredLongReads(RNABloom.java:3314)
        at rnabloom.RNABloom.main(RNABloom.java:7430)

from rna-bloom.

kmnip avatar kmnip commented on September 19, 2024

Hi @nityendra21 ,

Regarding your command:

rnabloom -long assembly/cleaned.reads.fastq -t 80 -mem 900 -o assembly/bloom

The -mem option is for setting the total size in GB allocated for the Bloom filters. You do not need to set this option. RNA-Bloom can set it for you automatically based on ntCard's output.

Regarding java.lang.OutOfMemoryError: Java heap space, you can set Java's maximum heap size with -Xmx. For example, to set it to 100GB:

export JAVA_TOOL_OPTIONS="-Xmx100g"
rnabloom -long assembly/cleaned.reads.fastq -t 80 -o assembly/bloom

If your RAM has 900GB and you set -mem 900, the Bloom filters will occupy your RAM entirely and it does not have any more memory left for computations using the Java heap space. That is the reason why you are getting the java.lang.OutOfMemoryError.

from rna-bloom.

nityendra21 avatar nityendra21 commented on September 19, 2024

Thank you for the quick reply @kmnip, I have run RNA-Bloom as suggested by you and will report back.

from rna-bloom.

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.