Dear all,
Here's the complete stack trace:
10:26:14,796 INFO Loader:296 - D:\AE000521.gbk is readable.
10:26:16,046 INFO Loader:340 - Alphabet of AE000521 is Empty Alphabet.
Skipping...
10:26:16,250 INFO Loader:296 - D:\AE004438.gbk is readable.
10:26:20,750 FATAL Loader:334 - Sequence AE004438 already exists.
10:26:20,921 INFO Loader:296 - D:\AE005174.gbk is readable.
10:26:28,328 INFO Loader:326 - Loading sequence AE005174 with
identifier 56384585, length 5528445 and alphabet DNA...
org.hibernate.PropertyAccessException: Exception occurred inside getter
of org.biojavax.bio.seq.SimpleRichSequence.sequenceLength
at
org.hibernate.property.BasicPropertyAccessor$BasicGetter.get(BasicPropertyAccessor.java:148)
at
org.hibernate.tuple.entity.AbstractEntityTuplizer.getPropertyValues(AbstractEntityTuplizer.java:256)
at
org.hibernate.tuple.entity.PojoEntityTuplizer.getPropertyValues(PojoEntityTuplizer.java:209)
at
org.hibernate.persister.entity.AbstractEntityPersister.getPropertyValues(AbstractEntityPersister.java:3581)
at
org.hibernate.event.def.DefaultMergeEventListener.copyValues(DefaultMergeEventListener.java:377)
at
org.hibernate.event.def.DefaultMergeEventListener.entityIsTransient(DefaultMergeEventListener.java:179)
at
org.hibernate.event.def.DefaultMergeEventListener.onMerge(DefaultMergeEventListener.java:123)
at
org.hibernate.event.def.DefaultMergeEventListener.onMerge(DefaultMergeEventListener.java:53)
at org.hibernate.impl.SessionImpl.fireMerge(SessionImpl.java:677)
at org.hibernate.impl.SessionImpl.merge(SessionImpl.java:661)
at ph.gov.dost.asti.genbankers.Loader.load(Loader.java:328)
at ph.gov.dost.asti.genbankers.Loader.<init>(Loader.java:137)
at ph.gov.dost.asti.genbankers.Loader.main(Loader.java:416)
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at
org.hibernate.property.BasicPropertyAccessor$BasicGetter.get(BasicPropertyAccessor.java:145)
... 12 more
Caused by: java.lang.NullPointerException
at
org.biojavax.bio.seq.SimpleRichSequence.length(SimpleRichSequence.java:91)
at
org.biojavax.bio.seq.SimpleRichSequence.getSequenceLength(SimpleRichSequence.java:97)
... 17 more
10:26:28,937 ERROR AbstractBatcher:51 - Exception executing batch:
org.hibernate.StaleStateException: Batch update returned unexpected row
count from update [0]; actual row count: 0; expected: 1
at
org.hibernate.jdbc.Expectations$BasicExpectation.checkBatched(Expectations.java:61)
at
org.hibernate.jdbc.Expectations$BasicExpectation.verifyOutcome(Expectations.java:46)
at
org.hibernate.jdbc.BatchingBatcher.checkRowCounts(BatchingBatcher.java:68)
at
org.hibernate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:48)
at
org.hibernate.jdbc.AbstractBatcher.executeBatch(AbstractBatcher.java:246)
at
org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:266)
at
org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:168)
at
org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:298)
at
org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:27)
at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000)
at ph.gov.dost.asti.genbankers.Loader.load(Loader.java:351)
at ph.gov.dost.asti.genbankers.Loader.<init>(Loader.java:137)
at ph.gov.dost.asti.genbankers.Loader.main(Loader.java:416)
10:26:28,937 ERROR AbstractFlushingEventListener:301 - Could not
synchronize database state with session
org.hibernate.StaleStateException: Batch update returned unexpected row
count from update [0]; actual row count: 0; expected: 1
at
org.hibernate.jdbc.Expectations$BasicExpectation.checkBatched(Expectations.java:61)
at
org.hibernate.jdbc.Expectations$BasicExpectation.verifyOutcome(Expectations.java:46)
at
org.hibernate.jdbc.BatchingBatcher.checkRowCounts(BatchingBatcher.java:68)
at
org.hibernate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:48)
at
org.hibernate.jdbc.AbstractBatcher.executeBatch(AbstractBatcher.java:246)
at
org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:266)
at
org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:168)
at
org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:298)
at
org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:27)
at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000)
at ph.gov.dost.asti.genbankers.Loader.load(Loader.java:351)
at ph.gov.dost.asti.genbankers.Loader.<init>(Loader.java:137)
at ph.gov.dost.asti.genbankers.Loader.main(Loader.java:416)
Exception in thread "main" org.hibernate.StaleStateException: Batch
update returned unexpected row count from update [0]; actual row count:
0; expected: 1
at
org.hibernate.jdbc.Expectations$BasicExpectation.checkBatched(Expectations.java:61)
at
org.hibernate.jdbc.Expectations$BasicExpectation.verifyOutcome(Expectations.java:46)
at
org.hibernate.jdbc.BatchingBatcher.checkRowCounts(BatchingBatcher.java:68)
at
org.hibernate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:48)
at
org.hibernate.jdbc.AbstractBatcher.executeBatch(AbstractBatcher.java:246)
at
org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:266)
at
org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:168)
at
org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:298)
at
org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:27)
at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000)
at ph.gov.dost.asti.genbankers.Loader.load(Loader.java:351)
at ph.gov.dost.asti.genbankers.Loader.<init>(Loader.java:137)
at ph.gov.dost.asti.genbankers.Loader.main(Loader.java:416)
Richard Holland wrote:
Hmm in that case it must be something else.
Your original mail only posted the first couple of lines of the stack
trace. Could you post the whole thing so we can take a closer look?
2008/7/18 Mark Schreiber <[EMAIL PROTECTED]>:
Was looking on the internet ...
So the Java spec says nothing about an upper limit however the sun JDK
implements String as a char[] (behind the scenes). Therefore I think
that on the Sun JDK with the right amount of RAM you could go to 2^32
(except for string literals as mentioned above) which is 4,294,967,296
characters. So a string of a sequence should be able to get to about 4
billion bases.
Of course if you don't assign enough memory to the JVM ( -Xmx4G) you
won't be able to get close. Of course even if you can assign that much
that doesn't account for all the other Java overhead and all the stuff
Hibernate is doing with proxy classes etc. Also BioSQL usually
defines sequence as a CLOB so depending on your DB implementation
there may be a limit on that. On a 32 bit machine 4GB is all you can
get per CPU so you would have issues trying to do anything bigger.
Anyhow I know I have stored human chromosome 1 (approx 1 billion bases
in memory).
- Mark
On Fri, Jul 18, 2008 at 6:45 PM, James Carman
<[EMAIL PROTECTED]> wrote:
That is a limitation for string literals, not any string. Correct?
On Fri, Jul 18, 2008 at 4:47 AM, Richard Holland
<[EMAIL PROTECTED]> wrote:
In order to persist to BioSQL, BioJava has to convert the symbol list
into a string so that it can pass it to JDBC via Hibernate. Therefore
the maximum length of a sequence you wish to persist to BioSQL is the
maximum length of a string in Java, which is 65536 (2^16) if you are
working in a UTF-8 environment.
2008/7/18 Rey Vincent Babilonia <[EMAIL PROTECTED]>:
Hi Mark,
What is the maximum sequence length that a RichSequence can handle?
java -Xms1024m -Xmx1256m -jar loader.jar
.
16:09:00,173 INFO Loader:296 - D:\AE005174.gbk is readable.
16:09:06,704 INFO Loader:326 - Loading sequence AE005174 with identifier
56384585, length 5528445 and alphabet DNA...
org.hibernate.PropertyAccessException: Exception occurred inside getter of
org.biojavax.bio.seq.SimpleRichSequence.sequenceLength
Rey Vincent Babilonia wrote:
Hi Mark,
At first it throws an out of memory exception. My workaround is to
subdivide the sequence file into individual GenBank files.
The error now is that if a GenBank sequence has an 'empty alphabet', it
does not get loaded to BioSQL. My workaround is to check if
sequence.getAlphabet().getName() is DNA.
Thanks.
Mark Schreiber wrote:
Hi -
Is the code throwing an exception or running out of memory??
Can you send an example program and the problem you encounter to the
list.
- Mark
On Thu, May 29, 2008 at 9:53 AM, Rey Vincent Babilonia
<[EMAIL PROTECTED]> wrote:
-------- Original Message --------
Subject: large genbank data
Date: Wed, 28 May 2008 18:02:48 +0800
From: Rey Vincent Babilonia <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]
hi,
anybody tried uploading a large genbank data (e.g.
ftp://bio-mirror.net/biomirror/genbank/gbbct1.seq.gz) to biosql?
load_seqdatabase.pl of bioperl can do this. i'm switching to biojava and
it can't read the sequence (maybe because it has 30000+ sequences).
thanks.
--
/**
* @author Rey Vincent P. Babilonia
* @number +63 2 426 9760 local 1302
* @pgp 0x383454CF <at> pgp.mit.edu
* @project Philippine Bioinformatics Solutions
* @program Philippine e-Science Grid
* @division Research and Development Division
* @agency Advanced Science and Technology Institute
* @url http://www.psigrid.gov.ph
*/
--
/**
* @author Rey Vincent P. Babilonia
* @number +63 2 426 9760 local 1302
* @pgp 0x383454CF <at> pgp.mit.edu
* @project Philippine Bioinformatics Solutions
* @program Philippine e-Science Grid
* @division Research and Development Division
* @agency Advanced Science and Technology Institute
* @url http://www.psigrid.gov.ph
*/
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/**
* @author Rey Vincent P. Babilonia
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* @pgp 0x383454CF <at> pgp.mit.edu
* @project Philippine Bioinformatics Solutions
* @program Philippine e-Science Grid
* @division Research and Development Division
* @agency Advanced Science and Technology Institute
* @url http://www.psigrid.gov.ph
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/**
* @author Rey Vincent P. Babilonia
* @number +63 2 426 9760 local 1302
* @pgp 0x383454CF <at> pgp.mit.edu
* @project Philippine Bioinformatics Solutions
* @program Philippine e-Science Grid
* @division Research and Development Division
* @agency Advanced Science and Technology Institute
* @url http://www.psigrid.gov.ph
*/
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