Hello, Works perfect now!!! Thanks for looking into it.
On 8/8/06, Richard Holland <[EMAIL PROTECTED]> wrote: > > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Hello all. > > Sorry for the delay - I was off sick yesterday. > > The bug had been fixed in the BioSQL side of things, but not when merely > loading sequences into memory without persisting them to the database. > I've been through and checked and hopefully fixed this now in CVS. Let > me know how you get on! > > cheers, > Richard > > > David Scott wrote: > > hi seth- > > > > nm_006145 loaded for me and i recreated the genbank entry with only > > minor differences - now, i'm at a loss - maybe we should wait for the > > other guys to get online after the weekend - they are much better at > > this remote debugging than i am. > > > > sorry i just couldn't help- > > david > > > > Seth Johnson wrote: > >> Hi David, > >> > >> I compiled my biojava.jar on 7/28 and, just to make sure, I've updated > >> my biojava-live cvs just now and it doesn't look like there were any > >> changes made since that date. The SimpleDocRef.java was last updated > >> on 7/18 and the version that I have does include the second > >> constructor with 2 parameters. It seems to be related to null TITLE > >> since all of the entries are missing it, but I was also under the > >> impression that null TITLE issue was fixed. That's what is so puzzling > >> about this. Below is the list of the problem accession IDs if you'd > >> like to replicate the exception: > >> > >> NM_006145 > >> NM_000602 > >> NM_006226 > >> NM_000371 > >> NM_019072 > >> NM_017884 > >> NM_022107 > >> NM_031418 > >> NM_030809 > >> NM_032731 > >> NM_001029888 > >> NM_001029869 > >> NM_182572 > >> > >> On 8/4/06, *David Scott* <[EMAIL PROTECTED] > >> <mailto:[EMAIL PROTECTED]>> wrote: > >> > >> 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 > >> > > >> > > >> > > >> > > >> > > >> > >> > >> > >> > >> -- > >> Best Regards, > >> > >> > >> Seth Johnson > >> Senior Bioinformatics Associate > >> > >> Ph: (202) 470-0900 > >> Fx: (775) 251-0358 > > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.2.2 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iD8DBQFE2E8K4C5LeMEKA/QRAsZlAKCUyzOv2z94PViXbx2i3RVTXCfn1gCfbxEU > oCGhefHeLFUxIrHLgZJHuQ0= > =SMVh > -----END PGP SIGNATURE----- > -- Best Regards, Seth Johnson Senior Bioinformatics Associate Ph: (202) 470-0900 Fx: (775) 251-0358 _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
