8000 Annotation error: Exception in thread "main" java.lang.NullPointerException · Issue #12 · mulinlab/VarNote · GitHub
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Annotation error: Exception in thread "main" java.lang.NullPointerException#12
@chrisclarkson

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@chrisclarkson
chrisclarkson
opened on Nov 25, 2020

Hello,
I would like to use VarNote to annotate a test vcf file with the gnomad.
However I get an error that I can't really interpret- Exception in thread "main" java.lang.NullPointerException

Here is what I have tried:

java -jar VarNote-1.1.0.jar Annotation -Q test.vcf.gz -D:db,tag=gnomAD,mode=1 http://202.113.53.226/VarNoteDB/VarNoteDB_AF_gnomAD_Genome.vcf.gz  -A all_dbs.annoc -O ./q1.sort.vcf.remote.anno.gz

No output file results and the output message is this:

14:45:45.114 INFO  LoggingUtils - 

----------------------------------------------------            QUERY            ----------------------------------------------------
14:45:45.128 INFO  LoggingUtils - Query File: test.vcf.gz
14:45:45.128 INFO  LoggingUtils - Query Format: VCF
14:45:45.129 INFO  LoggingUtils - Query header is: CHROM        POS     ID      REF     ALT     QUAL    FILTER  INFO      FORMAT  NA18486 NA18488 NA18489 NA18498 NA18499 NA18501 NA18502 NA18504 NA18505 NA18507 NA18508 NA18510 NA18511   NA18516 NA18517 NA18519 NA18520 NA18522 NA18523 NA18853 NA18856 NA18858 NA18861 NA18864 NA18865 NA18867 NA18868   NA18870 NA18871 NA18873 NA18874 NA18876 NA18877 NA18878 NA18879 NA18881 NA18907 NA18908 NA18909 NA18910 NA18912   NA18915 NA18916 NA18917 NA18923 NA18924 NA18933 NA18934 NA19092 NA19093 NA19095 NA19096 NA19098 NA19099 NA19102   NA19107 NA19108 NA19113 NA19114 NA19116 NA19117 NA19118 NA19119 NA19121 NA19129 NA19130 NA19131 NA19137 NA19138   NA19141 NA19143 NA19144 NA19146 NA19147 NA19149 NA19152 NA19153 NA19159 NA19160 NA19171 NA19172 NA19175 NA19184   NA19185 NA19189 NA19190 NA19197 NA19198 NA19200 NA19201 NA19204 NA19206 NA19207 NA19209 NA19210 NA19213 NA19214   NA19222 NA19223 NA19225 NA19235 NA19236 NA19238 NA19239 NA19247 NA19248 NA19256 NA19257
java.net.SocketException: Connection reset
        at java.net.SocketInputStream.read(SocketInputStream.java:209)
        at java.net.SocketInputStream.read(SocketInputStream.java:141)
        at java.io.BufferedInputStream.fill(BufferedInputStream.java:246)
        at java.io.BufferedInputStream.read1(BufferedInputStream.java:286)
        at java.io.BufferedInputStream.read(BufferedInputStream.java:345)
        at sun.net.www.http.HttpClient.parseHTTPHeader(HttpClient.java:704)
        at sun.net.www.http.HttpClient.parseHTTP(HttpClient.java:647)
        at sun.net.www.http.HttpClient.parseHTTP(HttpClient.java:675)
        at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1535)
        at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1440)
        at htsjdk.samtools.seekablestream.SeekableHTTPStream.read(SeekableHTTPStream.java:127)
        at java.io.BufferedInputStream.fill(BufferedInputStream.java:246)
        at java.io.BufferedInputStream.read1(BufferedInputStream.java:286)
        at java.io.BufferedInputStream.read(BufferedInputSt
6945
ream.java:345)
        at htsjdk.samtools.seekablestream.SeekableBufferedStream.read(SeekableBufferedStream.java:133)
        at java.io.InputStream.read(InputStream.java:101)
        at org.mulinlab.varnote.utils.VannoUtils.getAddress(VannoUtils.java:483)
        at org.mulinlab.varnote.utils.database.index.IndexFactory.readIndex(IndexFactory.java:38)
        at org.mulinlab.varnote.utils.database.Database.readIndex(Database.java:51)
        at org.mulinlab.varnote.utils.database.DatabaseFactory.readDatabase(DatabaseFactory.java:55)
        at org.mulinlab.varnote.utils.database.DatabaseFactory.readDatabaseFromConfig(DatabaseFactory.java:25)
        at org.mulinlab.varnote.config.run.RunConfig.init(RunConfig.java:48)
        at org.mulinlab.varnote.utils.RunFactory.run(RunFactory.java:133)
        at org.mulinlab.varnote.cmdline.tools.Annotation.doWork(Annotation.java:50)
        at org.mulinlab.varnote.cmdline.abstractclass.CMDProgram.runTool(CMDProgram.java:25)
        at org.mulinlab.varnote.cmdline.abstractclass.CMDProgram.instanceMain(CMDProgram.java:36)
        at org.mulinlab.varnote.cmdline.VarNoteCommandLine.instanceMain(VarNoteCommandLine.java:49)
        at org.mulinlab.varnote.cmdline.VarNoteCommandLine.main(VarNoteCommandLine.java:40)
java.net.SocketException: Connection reset
        at java.net.SocketInputStream.read(SocketInputStream.java:209)
        at java.net.SocketInputStream.read(SocketInputStream.java:141)
        at java.io.BufferedInputStream.fill(BufferedInputStream.java:246)
        at java.io.BufferedInputStream.read1(BufferedInputStream.java:286)
        at java.io.BufferedInputStream.read(BufferedInputStream.java:345)
        at sun.net.www.http.HttpClient.parseHTTPHeader(HttpClient.java:704)
        at sun.net.www.http.HttpClient.parseHTTP(HttpClient.java:647)
        at sun.net.www.http.HttpClient.parseHTTP(HttpClient.java:675)
        at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1535)
        at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1440)
        at htsjdk.samtools.seekablestream.SeekableHTTPStream.read(SeekableHTTPStream.java:127)
        at java.io.BufferedInputStream.fill(BufferedInputStream.java:246)
        at java.io.BufferedInputStream.read1(BufferedInputStream.java:286)
        at java.io.BufferedInputStream.read(BufferedInputStream.java:345)
        at htsjdk.samtools.seekablestream.SeekableBufferedStream.read(SeekableBufferedStream.java:133)
        at htsjdk.samtools.util.BlockCompressedInputStream.readBytes(BlockCompressedInputStream.java:571)
        at htsjdk.samtools.util.BlockCompressedInputStream.readBytes(BlockCompressedInputStream.java:560)
        at htsjdk.samtools.util.BlockCompressedInputStream.processNextBlock(BlockCompressedInputStream.java:510)
        at htsjdk.samtools.util.BlockCompressedInputStream.nextBlock(BlockCompressedInputStream.java:468)
        at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:458)
        at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:196)
        at htsjdk.samtools.util.BlockCompressedInputStream.seek(BlockCompressedInputStream.java:382)
        at org.mulinlab.varnote.utils.database.index.IndexFactory.readIndex(IndexFactory.java:39)
        at org.mulinlab.varnote.utils.database.Database.readIndex(Database.java:51)
        at org.mulinlab.varnote.utils.database.DatabaseFactory.readDatabase(DatabaseFactory.java:55)
        at org.mulinlab.varnote.utils.database.DatabaseFactory.readDatabaseFromConfig(DatabaseFactory.java:25)
        at org.mulinlab.varnote.config.run.RunConfig.init(RunConfig.java:48)
        at org.mulinlab.varnote.utils.RunFactory.run(RunFactory.java:133)
        at org.mulinlab.varnote.cmdline.tools.Annotation.doWork(Annotation.java:50)
        at org.mulinlab.varnote.cmdline.abstractclass.CMDProgram.runTool(CMDProgram.java:25)
        at org.mulinlab.varnote.cmdline.abstractclass.CMDProgram.instanceMain(CMDProgram.java:36)
        at org.mulinlab.varnote.cmdline.VarNoteCommandLine.instanceMain(VarNoteCommandLine.java:49)
        at org.mulinlab.varnote.cmdline.VarNoteCommandLine.main(VarNoteCommandLine.java:40)
Exception in thread "main" java.lang.NullPointerException
        at org.mulinlab.varnote.utils.database.Database.readIndex(Database.java:52)
        at org.mulinlab.varnote.utils.database.DatabaseFactory.readDatabase(DatabaseFactory.java:55)
        at org.mulinlab.varnote.utils.database.DatabaseFactory.readDatabaseFromConfig(DatabaseFactory.java:25)
        at org.mulinlab.varnote.config.run.RunConfig.init(RunConfig.java:48)
        at org.mulinlab.varnote.utils.RunFactory.run(RunFactory.java:133)
        at org.mulinlab.varnote.cmdline.tools.Annotation.doWork(Annotation.java:50)
        at org.mulinlab.varnote.cmdline.abstractclass.CMDProgram.runTool(CMDProgram.java:25)
        at org.mulinlab.varnote.cmdline.abstractclass.CMDProgram.instanceMain(CMDProgram.java:36)
        at org.mulinlab.varnote.cmdline.VarNoteCommandLine.instanceMain(VarNoteCommandLine.java:49)
        at org.mulinlab.varnote.cmdline.VarNoteCommandLine.main(VarNoteCommandLine.java:40)

The vcf file looks as follows:

##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20150218
##reference=ftp://ftp.1000genomes.ebi.ac.uk//vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d
##source=1000GenomesPhase3Pipeline
##contig=<ID=1,assembly=b37,length=249250621>
.....
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    NA18486 NA18488 NA18489 NA18498 ......
3       60069   rs549251461     C       T       100     PASS    AC=0;AF=0.000199681;AN=216;NS=2504;DP=10809;EAS_AF
3       60079   rs567712286     A       G       100     PASS    AC=0;AF=0.000399361;AN=216;NS=2504;DP=12198;EAS_AF
3       60157   rs186476240     G       A       100     PASS    AC=0;AF=0.000798722;AN=216;NS=2504;DP=15216;EAS_AF
3       60189   rs550163140     A       G       100     PASS    AC=0;AF=0.000199681;AN=216;NS=2504;DP=14835;EAS_AF
.....

The all_dbs.annoc file is copied and pasted from your example in the documentation:

@gnomAD
fields=[INFO]
info_fields=[AC, AF]
out_names=[AC:gnomAD_AC, AF:gnomAD_AF]

Is there something wrong with the way I'm doing this?

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