extra line return at the end of the fasta file causes extra space line error

[nathandunn]

The extra line return at the end of the fasta file causes extra space line error.

 File /opt/temporary/apollo/113449-uploadme does not exist
2019-08-20 09:47:44,679 [http-nio-8080-exec-8] WARN  apollo.TrackService  - File /opt/temporary/apollo/113449-uploadme can not be read
2019-08-20 09:47:44,679 [http-nio-8080-exec-8] WARN  apollo.TrackService  - File /opt/temporary/apollo/113449-uploadme can not be written to
search db file : searchDatabaseData 0  application/octet-stream
search file: /opt/temporary/apollo/113449-uploadme/search
| Error WARNING	2019-08-20 09:47:44	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
2019-08-20 09:47:46,276 [http-nio-8080-exec-8] WARN  apollo.PreferenceService  - Multiple preferences found: 3
2019-08-20 09:47:49,891 [http-nio-8080-exec-7] INFO  apollo.UserController  - updateTrackListPreference
2019-08-20 09:47:49,896 [http-nio-8080-exec-7] INFO  apollo.UserController  - Added userOrganismPreference false
| Error 2019-08-20 09:47:50,741 [http-nio-8080-exec-6] ERROR apollo.JbrowseController  - File not found: /opt/temporary/apollo/113449-uploadme/tracks.conf
| Error 2019-08-20 09:47:51,076 [http-nio-8080-exec-4] ERROR apollo.JbrowseController  - File not found: /opt/temporary/apollo/113449-uploadme/names/root.json
2019-08-20 09:48:08,554 [http-nio-8080-exec-3] WARN  apollo.TrackService  - File /opt/temporary/apollo/113493-upload2 does not exist
2019-08-20 09:48:08,554 [http-nio-8080-exec-3] WARN  apollo.TrackService  - File /opt/temporary/apollo/113493-upload2 can not be read
2019-08-20 09:48:08,554 [http-nio-8080-exec-3] WARN  apollo.TrackService  - File /opt/temporary/apollo/113493-upload2 can not be written to
search db file : searchDatabaseData 0  application/octet-stream
search file: /opt/temporary/apollo/113493-upload2/search
| Error WARNING	2019-08-20 09:48:08	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
| Error java.lang.StringIndexOutOfBoundsException: String index out of range: 0
| Error 	at java.lang.String.charAt(String.java:658)
| Error 	at htsjdk.samtools.reference.FastaSequenceIndexCreator.buildFromFasta(FastaSequenceIndexCreator.java:112)
| Error 	at htsjdk.samtools.reference.FastaSequenceIndexCreator.create(FastaSequenceIndexCreator.java:64)
| Error 	at htsjdk.samtools.reference.FastaSequenceIndexCreator$create.call(Unknown Source)
| Error 	at org.bbop.apollo.OrganismController.$tt__addOrganismWithSequence(OrganismController.groovy:370)
| Error 	at org.bbop.apollo.OrganismController$_addOrganismWithSequence_closure3.doCall(OrganismController.groovy)
| Error 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
| Error 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
| Error 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
| Error 	at java.lang.reflect.Method.invoke(Method.java:498)
| Error 	at org.springsource.loaded.ri.ReflectiveInterceptor.jlrMethodInvoke(ReflectiveInterceptor.java:1426)
| Error 	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
| Error 	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
| Error 	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1210)
| Error 	at groovy.lang.ExpandoMetaClass.invokeMethod(ExpandoMetaClass.java:1123)
| Error 	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1019)
| Error 	at groovy.lang.Closure.call(Closure.java:426)
| Error 	at org.bbop.apollo.OrganismController$_addOrganismWithSequence_closure3.call(OrganismController.groovy)
| Error 	at groovy.lang.Closure.call(Closure.java:442)
| Error 	at org.bbop.apollo.OrganismController$_addOrganismWithSequence_closure3.call(OrganismController.groovy)
| Error 	at org.codehaus.groovy.grails.orm.support.GrailsTransactionTemplate$2.doInTransaction(GrailsTransactionTemplate.groovy:90)
| Error 	at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:133)
| Error 	at org.codehaus.groovy.grails.orm.support.GrailsTransactionTemplate.execute(GrailsTransactionTemplate.groovy:87)
| Error 	at org.bbop.apollo.OrganismController.addOrganismWithSequence(OrganismController.groovy)
| Error 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
| Error 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
| Error 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
| Error 	at java.lang.reflect.Method.invoke(Method.java:498)
| Error 	at org.springsource.loaded.ri.ReflectiveInterceptor.jlrMethodInvoke(ReflectiveInterceptor.java:1426)