vadimzalunin/crammer — Issue #14: Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
Author: www1234
Created: 2012-02-23 19:35:13+00:00
State: open

> java -jar cramtools_06_reffix_30_1_12.jar bam --input-cram-file NA12882_CSS2_merged_nu_inssub.cram --reference-fasta-file HumanNCBI37Fasta.fa --output-bam-file NA12882_CSS2_merged_nu_inssub.bam

gives:

Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at java.util.Arrays.copyOf(Arrays.java:2746)
at java.util.ArrayList.ensureCapacity(ArrayList.java:187)
at java.util.ArrayList.add(ArrayList.java:378)
at uk.ac.ebi.ena.sra.cram.encoding.ReadFeatureCodec.read(ReadFeatureCodec.java:78)
at uk.ac.ebi.ena.sra.cram.encoding.ReadFeatureCodec.read(ReadFeatureCodec.java:20)
at uk.ac.ebi.ena.sra.cram.encoding.CramRecordCodec.read(CramRecordCodec.java:91)
at uk.ac.ebi.ena.sra.cram.encoding.CramRecordCodec.read(CramRecordCodec.java:16)
at uk.ac.ebi.ena.sra.cram.impl.SequentialCramReader.readRecord(SequentialCramReader.java:85)
at uk.ac.ebi.ena.sra.cram.Cram2Bam.convert(Cram2Bam.java:204)
at uk.ac.ebi.ena.sra.cram.Cram2Bam.main(Cram2Bam.java:105)
at uk.ac.ebi.ena.sra.cram.CramTools.main(CramTools.java:54)