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getting error while running map and assemble #7

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shanmugavadivelps opened this issue Nov 11, 2021 · 2 comments
Open

getting error while running map and assemble #7

shanmugavadivelps opened this issue Nov 11, 2021 · 2 comments

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@shanmugavadivelps
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shanmugavadivelps commented Nov 11, 2021 •
edited
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I could run .jar but getting error
java -jar /home/shanmu/VirGenA/release_v1.4/VirGenA.jar assemble -c /home/shanmu/VirGenA/release_v1.4/config.xml
Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
at java.io.BufferedReader.readLine(BufferedReader.java:356)
at java.io.BufferedReader.readLine(BufferedReader.java:389)
at DataReader.readFilesWithReads(DataReader.java:144)
at DataReader.readData(DataReader.java:41)
at DataReader.(DataReader.java:75)
at DataReader.getInstance(DataReader.java:102)
at KMerCounter.(KMerCounter.java:17)
at KMerCounter.getInstance(KMerCounter.java:59)
at Mapper.(Mapper.java:29)
at ConsensusBuilderSimple.(ConsensusBuilderSimple.java:23)
at ConsensusBuilderWithReassembling.(ConsensusBuilderWithReassembling.java:41)
at RefBasedAssembler.run(RefBasedAssembler.java:665)
at VirGenA.main(VirGenA.java:34)

java -jar /home/shanmu/VirGenA/release_v1.4/VirGenA.jar assemble -c /home/shanmu/VirGenA/release_v1.4/config.xml
Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
at java.lang.StringCoding$StringEncoder.encode(StringCoding.java:300)
at java.lang.StringCoding.encode(StringCoding.java:344)
at java.lang.StringCoding.encode(StringCoding.java:387)
at java.lang.String.getBytes(String.java:958)
at DataReader.readFilesWithReads(DataReader.java:152)
at DataReader.readData(DataReader.java:41)
at DataReader.(DataReader.java:75)
at DataReader.getInstance(DataReader.java:102)
at KMerCounter.(KMerCounter.java:17)
at KMerCounter.getInstance(KMerCounter.java:59)
at Mapper.(Mapper.java:29)
at ConsensusBuilderSimple.(ConsensusBuilderSimple.java:23)
at ConsensusBuilderWithReassembling.(ConsensusBuilderWithReassembling.java:41)
at RefBasedAssembler.run(RefBasedAssembler.java:665)
at VirGenA.main(VirGenA.java:34)

Pls help me to solve
@shanmugavadivelps shanmugavadivelps changed the title Editing XML file getting error while running map and assemble Nov 11, 2021
@gFedonin
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gFedonin commented Jan 4, 2022

Hello! Sorry for the late answer: I've missed the question somehow. Have you tried adding -Xmx30G option to java? By default it use only 4Gb. The full command will look like:

java -Xmx30G -jar /home/shanmu/VirGenA/release_v1.4/VirGenA.jar assemble -c /home/shanmu/VirGenA/release_v1.4/config.xml

If this doesn't help, please tell me more details: the genome length, the read length, the number of reads.

@shanmugavadivelps
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shanmugavadivelps commented Jul 8, 2022 •
edited
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I have run the command as follows
java -Xmx35G -jar /home/iipruser/VirGenA_v1.4/VirGenA.jar assemble -c /home/iipruser/VirGenA_v1.4/config_test_linux.xml

but again getting error

DEBUG 2022-07-08 10:22:43 BlockCompressedOutputStream Using deflater: Deflater

genome size 138 kb, read length:71-150 bases, paired end reads; total reads: 1.8 million reads.

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@gFedonin @shanmugavadivelps