hi seth- the 3rd argument to SimpleDocRef constructor is the REFERENCE title - which appears to be null in the trace - which happens, but rarely. i had the exact same problem recently - and richard put in code to check for a null title and then call a special 2 argument constructor for SimpleDocRef - any chance you don't have that code checked out?
best- david Seth Johnson wrote: > Hi Richard, > > > I'm back for more help. I've just completed getting and parsing the entire > human genome RefSeq list from NCBI. I'm not going to post my source code > since the invoking code has been described by the gentlemen who started the > original thread last month. The result of the parsing is such that out of > ~28K sequences, 13 produced the exceptions below. I've used the latest > biojava code from CVS, not quite sure what the problem is on these 13. > > > > Trying to get: NM_006145 > > org.biojava.bio.BioException: Failed to read Genbank sequence > > at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > GenbankRichSequenceDB.java:157) > > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java:162) > > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146) > > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195) > > Caused by: org.biojava.bio.BioException: Could not read sequence > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > RichStreamReader.java:112) > > at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > GenbankRichSequenceDB.java:153) > > ... 3 more > > Caused by: java.lang.IllegalArgumentException: Could not find constructor > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class > java.lang.String,null) > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > SimpleRichObjectBuilder.java:78) > > at org.biojavax.RichObjectFactory.getObject(RichObjectFactory.java > :104) > > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence( > GenbankFormat.java:387) > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > RichStreamReader.java:109) > > ... 4 more > > Caused by: java.lang.NullPointerException > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > SimpleRichObjectBuilder.java:59) > > ... 7 more > > org.biojava.bio.BioException: Failed to read Genbank sequence > > at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > GenbankRichSequenceDB.java:157) > > -------------------------------------------------------------------------------- > > Trying to get: NM_000602 > > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java:162) > > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146) > > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195) > > Caused by: org.biojava.bio.BioException: Could not read sequence > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > RichStreamReader.java:112) > > at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > GenbankRichSequenceDB.java:153) > > ... 3 more > > Caused by: java.lang.IllegalArgumentException: Could not find constructor > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class > java.lang.String,null) > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > SimpleRichObjectBuilder.java:78) > > at org.biojavax.RichObjectFactory.getObject(RichObjectFactory.java > :104) > > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence( > GenbankFormat.java:387) > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > RichStreamReader.java:109) > > ... 4 more > > Caused by: java.lang.NullPointerException > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > SimpleRichObjectBuilder.java:59) > > ... 7 more > > ------------------------------------------------------------------------------- > > Trying to get: NM_006226 > > org.biojava.bio.BioException: Failed to read Genbank sequence > > at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > GenbankRichSequenceDB.java:157) > > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java:162) > > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146) > > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195) > > Caused by: org.biojava.bio.BioException: Could not read sequence > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > RichStreamReader.java:112) > > at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > GenbankRichSequenceDB.java:153) > > ... 3 more > > Caused by: java.lang.IllegalArgumentException: Could not find constructor > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class > java.lang.String,null) > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > SimpleRichObjectBuilder.java:78) > > at org.biojavax.RichObjectFactory.getObject(RichObjectFactory.java > :104) > > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence( > GenbankFormat.java:387) > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > RichStreamReader.java:109) > > ... 4 more > > Caused by: java.lang.NullPointerException > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > SimpleRichObjectBuilder.java:59) > > ... 7 more > > ---------------------------------------------------------------------------------- > > Trying to get: NM_000371 > > org.biojava.bio.BioException: Failed to read Genbank sequence > > at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > GenbankRichSequenceDB.java:157) > > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java:162) > > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146) > > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195) > > Caused by: org.biojava.bio.BioException: Could not read sequence > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > RichStreamReader.java:112) > > at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > GenbankRichSequenceDB.java:153) > > ... 3 more > > Caused by: java.lang.IllegalArgumentException: Could not find constructor > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class > java.lang.String,null) > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > SimpleRichObjectBuilder.java:78) > > at org.biojavax.RichObjectFactory.getObject(RichObjectFactory.java > :104) > > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence( > GenbankFormat.java:387) > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > RichStreamReader.java:109) > > ... 4 more > > Caused by: java.lang.NullPointerException > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > SimpleRichObjectBuilder.java:59) > > ... 7 more > > -------------------------------------------------------------------------------- > > Trying to get: NM_019072 > > org.biojava.bio.BioException: Failed to read Genbank sequence > > at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > GenbankRichSequenceDB.java:157) > > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java:162) > > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146) > > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195) > > Caused by: org.biojava.bio.BioException: Could not read sequence > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > RichStreamReader.java:112) > > at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > GenbankRichSequenceDB.java:153) > > ... 3 more > > Caused by: java.lang.IllegalArgumentException: Could not find constructor > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class > java.lang.String,null) > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > SimpleRichObjectBuilder.java:78) > > at org.biojavax.RichObjectFactory.getObject(RichObjectFactory.java > :104) > > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence( > GenbankFormat.java:387) > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > RichStreamReader.java:109) > > ... 4 more > > Caused by: java.lang.NullPointerException > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > SimpleRichObjectBuilder.java:59) > > ... 7 more > > -------------------------------------------------------------------------------- > > Trying to get: NM_017884 > > org.biojava.bio.BioException: Failed to read Genbank sequence > > at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > GenbankRichSequenceDB.java:157) > > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java:162) > > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146) > > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195) > > Caused by: org.biojava.bio.BioException: Could not read sequence > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > RichStreamReader.java:112) > > at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > GenbankRichSequenceDB.java:153) > > ... 3 more > > Caused by: java.lang.IllegalArgumentException: Could not find constructor > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class > java.lang.String,null) > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > SimpleRichObjectBuilder.java:78) > > at org.biojavax.RichObjectFactory.getObject(RichObjectFactory.java > :104) > > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence( > GenbankFormat.java:387) > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > RichStreamReader.java:109) > > ... 4 more > > Caused by: java.lang.NullPointerException > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > SimpleRichObjectBuilder.java:59) > > ... 7 more > > -------------------------------------------------------------------------------- > > Trying to get: NM_022107 > > org.biojava.bio.BioException: Failed to read Genbank sequence > > at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > GenbankRichSequenceDB.java:157) > > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java:162) > > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146) > > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195) > > Caused by: org.biojava.bio.BioException: Could not read sequence > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > RichStreamReader.java:112) > > at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > GenbankRichSequenceDB.java:153) > > ... 3 more > > Caused by: java.lang.IllegalArgumentException: Could not find constructor > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class > java.lang.String,null) > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > SimpleRichObjectBuilder.java:78) > > at org.biojavax.RichObjectFactory.getObject(RichObjectFactory.java > :104) > > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence( > GenbankFormat.java:387) > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > RichStreamReader.java:109) > > ... 4 more > > Caused by: java.lang.NullPointerException > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > SimpleRichObjectBuilder.java:59) > > ... 7 more > > --------------------------------------------------------------------------------- > > Trying to get: NM_031418 > > org.biojava.bio.BioException: Failed to read Genbank sequence > > at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > GenbankRichSequenceDB.java:157) > > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java:162) > > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146) > > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195) > > Caused by: org.biojava.bio.BioException: Could not read sequence > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > RichStreamReader.java:112) > > at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > GenbankRichSequenceDB.java:153) > > ... 3 more > > Caused by: java.lang.IllegalArgumentException: Could not find constructor > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class > java.lang.String,null) > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > SimpleRichObjectBuilder.java:78) > > at org.biojavax.RichObjectFactory.getObject(RichObjectFactory.java > :104) > > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence( > GenbankFormat.java:387) > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > RichStreamReader.java:109) > > ... 4 more > > Caused by: java.lang.NullPointerException > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > SimpleRichObjectBuilder.java:59) > > ... 7 more > > --------------------------------------------------------------------------------------- > > Trying to get: NM_030809 > > org.biojava.bio.BioException: Failed to read Genbank sequence > > at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > GenbankRichSequenceDB.java:157) > > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java:162) > > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146) > > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195) > > Caused by: org.biojava.bio.BioException: Could not read sequence > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > RichStreamReader.java:112) > > at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > GenbankRichSequenceDB.java:153) > > ... 3 more > > Caused by: java.lang.IllegalArgumentException: Could not find constructor > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class > java.lang.String,null) > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > SimpleRichObjectBuilder.java:78) > > at org.biojavax.RichObjectFactory.getObject(RichObjectFactory.java > :104) > > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence( > GenbankFormat.java:387) > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > RichStreamReader.java:109) > > ... 4 more > > Caused by: java.lang.NullPointerException > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > SimpleRichObjectBuilder.java:59) > > ... 7 more > > ------------------------------------------------------------------------------------- > > Trying to get: NM_032731 > > org.biojava.bio.BioException: Failed to read Genbank sequence > > at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > GenbankRichSequenceDB.java:157) > > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java:162) > > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146) > > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195) > > Caused by: org.biojava.bio.BioException: Could not read sequence > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > RichStreamReader.java:112) > > at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > GenbankRichSequenceDB.java:153) > > ... 3 more > > Caused by: java.lang.IllegalArgumentException: Could not find constructor > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class > java.lang.String,null) > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > SimpleRichObjectBuilder.java:78) > > at org.biojavax.RichObjectFactory.getObject(RichObjectFactory.java > :104) > > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence( > GenbankFormat.java:387) > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > RichStreamReader.java:109) > > ... 4 more > > Caused by: java.lang.NullPointerException > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > SimpleRichObjectBuilder.java:59) > > ... 7 more > > ------------------------------------------------------------------------------------ > > Trying to get: NM_001029888 > > org.biojava.bio.BioException: Failed to read Genbank sequence > > at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > GenbankRichSequenceDB.java:157) > > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java:162) > > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146) > > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195) > > Caused by: org.biojava.bio.BioException: Could not read sequence > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > RichStreamReader.java:112) > > at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > GenbankRichSequenceDB.java:153) > > ... 3 more > > Caused by: java.lang.IllegalArgumentException: Could not find constructor > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class > java.lang.String,null) > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > SimpleRichObjectBuilder.java:78) > > at org.biojavax.RichObjectFactory.getObject(RichObjectFactory.java > :104) > > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence( > GenbankFormat.java:387) > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > RichStreamReader.java:109) > > ... 4 more > > Caused by: java.lang.NullPointerException > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > SimpleRichObjectBuilder.java:59) > > ... 7 more > > ------------------------------------------------------------------------------------ > > Trying to get: NM_001029869 > > org.biojava.bio.BioException: Failed to read Genbank sequence > > at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > GenbankRichSequenceDB.java:157) > > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java:162) > > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146) > > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195) > > Caused by: org.biojava.bio.BioException: Could not read sequence > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > RichStreamReader.java:112) > > at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > GenbankRichSequenceDB.java:153) > > ... 3 more > > Caused by: java.lang.IllegalArgumentException: Could not find constructor > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class > java.lang.String,null) > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > SimpleRichObjectBuilder.java:78) > > at org.biojavax.RichObjectFactory.getObject(RichObjectFactory.java > :104) > > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence( > GenbankFormat.java:387) > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > RichStreamReader.java:109) > > ... 4 more > > Caused by: java.lang.NullPointerException > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > SimpleRichObjectBuilder.java:59) > > ... 7 more > > ------------------------------------------------------------------------------------ > > Trying to get: NM_182572 > > org.biojava.bio.BioException: Failed to read Genbank sequence > > at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > GenbankRichSequenceDB.java:157) > > at exonhit.parsers.RefSeqParser.updateRefSeq(RefSeqParser.java:162) > > at exonhit.parsers.RefSeqParser.update(RefSeqParser.java:146) > > at exonhit.parsers.RefSeqParser.main(RefSeqParser.java:195) > > Caused by: org.biojava.bio.BioException: Could not read sequence > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > RichStreamReader.java:112) > > at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence( > GenbankRichSequenceDB.java:153) > > ... 3 more > > Caused by: java.lang.IllegalArgumentException: Could not find constructor > for class org.biojavax.SimpleDocRef(class java.util.ArrayList,class > java.lang.String,null) > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > SimpleRichObjectBuilder.java:78) > > at org.biojavax.RichObjectFactory.getObject(RichObjectFactory.java > :104) > > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence( > GenbankFormat.java:387) > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence( > RichStreamReader.java:109) > > ... 4 more > > Caused by: java.lang.NullPointerException > > at org.biojavax.SimpleRichObjectBuilder.buildObject( > SimpleRichObjectBuilder.java:59) > > ... 7 more > > > > > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
