Comments (4)
That worked excellently. Thank you @kmnip
from rna-bloom.
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.
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.
Thank you for the quick reply @kmnip, I have run RNA-Bloom as suggested by you and will report back.
from rna-bloom.
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