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java.lang.IllegalArgumentException: Invalid interval. #4712

Closed chatchawit closed 6 years ago

chatchawit commented 6 years ago

I've got this error.

java.lang.IllegalArgumentException: Invalid interval. Contig:ENST00000342066.7|ENSG00000187634.11|OTTHUMG00000040719.10|OTTHUMT00000276866.2|SAMD11-202|SAMD11|2551|protein_coding| start:0 end:0

I'm working on hg38. The VCF input file was produced from Mutect2.

First, I've the error "java.lang.NullPointerException". So I put only "gencode" folder in the data-source folder. Then, I've got the error message above.

lbergelson commented 6 years ago

Hi @chatchawit,

It's hard to tell what's going on from the information you provided. Could you include the exact commandline that you're trying to run. Also, the complete stack trace from both the original error and the new error message would be very helpful.

chatchawit commented 6 years ago

Here is the command line. I'm using funcotator_dataSources.v1.2.20180329.tar.gz. /omics/chatchawit/gatk/gatk Funcotator -R /omics/chatchawit/bundle/hsa38.fasta -V /omics/chatchawit/sm/out/sample21.vcf -O /omics/chatchawit/sm/anno/sample21.vcf --data-sources-path /omics/chatchawit/bundle/dsrc/ --ref-version hg38

Using GATK jar /omics/chatchawit/gatk/gatk-package-4.0.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=1 -jar /omics/chatchawit/gatk/gatk-package-4.0.0.0-local.jar Funcotator -R /omics/chatchawit/bundle/hsa38.fasta -V /omics/chatchawit/sm/out/sample21.vcf -O /omics/chatchawit/sm/anno/sample21.vcf --data-sources-path /omics/chatchawit/bundle/dsrc/ --ref-version hg38 22:56:54.836 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/omics/chatchawit/gatk/gatk-package-4.0.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 22:56:55.064 INFO Funcotator - ------------------------------------------------------------ 22:56:55.065 INFO Funcotator - The Genome Analysis Toolkit (GATK) v4.0.0.0 22:56:55.065 INFO Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/ 22:56:55.065 INFO Funcotator - Executing as chatchawit@omics on Linux v3.13.0-133-generic amd64 22:56:55.066 INFO Funcotator - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_161-b12 22:56:55.066 INFO Funcotator - Start Date/Time: April 27, 2018 10:56:54 PM ICT 22:56:55.066 INFO Funcotator - ------------------------------------------------------------ 22:56:55.066 INFO Funcotator - ------------------------------------------------------------ 22:56:55.067 INFO Funcotator - HTSJDK Version: 2.13.2 22:56:55.067 INFO Funcotator - Picard Version: 2.17.2 22:56:55.067 INFO Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 1 22:56:55.067 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 22:56:55.068 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 22:56:55.068 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 22:56:55.068 INFO Funcotator - Deflater: IntelDeflater 22:56:55.068 INFO Funcotator - Inflater: IntelInflater 22:56:55.068 INFO Funcotator - GCS max retries/reopens: 20 22:56:55.068 INFO Funcotator - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 22:56:55.068 INFO Funcotator - Initializing engine 22:56:56.227 INFO FeatureManager - Using codec VCFCodec to read file file:///omics/chatchawit/sm/out/sample21.vcf 22:56:56.402 INFO Funcotator - Done initializing engine 22:56:56.425 INFO Funcotator - Shutting down engine [April 27, 2018 10:56:56 PM ICT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=2276982784 java.lang.NullPointerException at org.broadinstitute.hellbender.tools.funcotator.Funcotator.closeTool(Funcotator.java:330) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:897) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:136) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:179) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:198) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:152) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:195) at org.broadinstitute.hellbender.Main.main(Main.java:275)

Next, I tried only "gencode" in the data-source folder.

Using GATK jar /omics/chatchawit/gatk/gatk-package-4.0.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=1 -jar /omics/chatchawit/gatk/gatk-package-4.0.0.0-local.jar Funcotator -R /omics/chatchawit/bundle/hsa38.fasta -V /omics/chatchawit/sm/out/sample21.vcf -O /omics/chatchawit/sm/anno/sample21.vcf --data-sources-path /omics/chatchawit/bundle/test/ --ref-version hg38 23:01:57.151 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/omics/chatchawit/gatk/gatk-package-4.0.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 23:01:57.341 INFO Funcotator - ------------------------------------------------------------ 23:01:57.341 INFO Funcotator - The Genome Analysis Toolkit (GATK) v4.0.0.0 23:01:57.341 INFO Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/ 23:01:57.342 INFO Funcotator - Executing as chatchawit@omics on Linux v3.13.0-133-generic amd64 23:01:57.342 INFO Funcotator - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_161-b12 23:01:57.342 INFO Funcotator - Start Date/Time: April 27, 2018 11:01:57 PM ICT 23:01:57.343 INFO Funcotator - ------------------------------------------------------------ 23:01:57.343 INFO Funcotator - ------------------------------------------------------------ 23:01:57.344 INFO Funcotator - HTSJDK Version: 2.13.2 23:01:57.344 INFO Funcotator - Picard Version: 2.17.2 23:01:57.344 INFO Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 1 23:01:57.344 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 23:01:57.344 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 23:01:57.344 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 23:01:57.344 INFO Funcotator - Deflater: IntelDeflater 23:01:57.344 INFO Funcotator - Inflater: IntelInflater 23:01:57.345 INFO Funcotator - GCS max retries/reopens: 20 23:01:57.345 INFO Funcotator - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 23:01:57.345 INFO Funcotator - Initializing engine 23:01:58.372 INFO FeatureManager - Using codec VCFCodec to read file file:///omics/chatchawit/sm/out/sample21.vcf 23:01:58.541 INFO Funcotator - Done initializing engine log4j:WARN No appenders could be found for logger (org.broadinstitute.hellbender.tools.funcotator.Funcotator). log4j:WARN Please initialize the log4j system properly. log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info. 23:01:58.560 INFO FeatureManager - Using codec GencodeGtfCodec to read file file:///omics/chatchawit/bundle/test/gencode/hg38/gencode.v27.chr_patch_hapl_scaff.annotation.REORDERED.gtf 23:02:05.335 INFO ProgressMeter - Starting traversal 23:02:05.337 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 23:02:06.530 INFO Funcotator - Shutting down engine [April 27, 2018 11:02:06 PM ICT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.16 minutes. Runtime.totalMemory()=3420979200 java.lang.IllegalArgumentException: Invalid interval. Contig:ENST00000342066.7|ENSG00000187634.11|OTTHUMG00000040719.10|OTTHUMT00000276866.2|SAMD11-202|SAMD11|2551|protein_coding| start:0 end:0 at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:687) at org.broadinstitute.hellbender.utils.SimpleInterval.validatePositions(SimpleInterval.java:61) at org.broadinstitute.hellbender.utils.SimpleInterval.(SimpleInterval.java:37) at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.getCodingSequenceFromTranscriptFasta(GencodeFuncotationFactory.java:418) at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createSequenceComparison(GencodeFuncotationFactory.java:1177) at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createCodingRegionFuncotation(GencodeFuncotationFactory.java:619) at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createGencodeFuncotationOnTranscript(GencodeFuncotationFactory.java:575) at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createFuncotations(GencodeFuncotationFactory.java:487) at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createFuncotations(GencodeFuncotationFactory.java:243) at org.broadinstitute.hellbender.tools.funcotator.Funcotator.enqueueAndHandleVariant(Funcotator.java:387) at org.broadinstitute.hellbender.tools.funcotator.Funcotator.apply(Funcotator.java:316) at org.broadinstitute.hellbender.engine.VariantWalkerBase.lambda$traverse$0(VariantWalkerBase.java:110) at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184) at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175) at java.util.Iterator.forEachRemaining(Iterator.java:116) at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801) at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481) at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471) at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151) at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174) at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418) at org.broadinstitute.hellbender.engine.VariantWalkerBase.traverse(VariantWalkerBase.java:108) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:893) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:136) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:179) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:198) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:152) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:195) at org.broadinstitute.hellbender.Main.main(Main.java:275)

If you need more info, please let me know. Thank you.

lbergelson commented 6 years ago

@chatchawit Thank you for the additional information, thats very helpful.
It looks like you're using gatk 4.0.0.0, there have a been a lot of updates to funcotator since then. I might try running with the newest release 4.0.4.0 and see if that resolves the problem.

@jonn-smith As the funcomaster, you may have some insight?

jonn-smith commented 6 years ago

@chatchawit Like Louis said, there have been quite a few updates.

The issue you're seeing is a data sources problem relating to HG38. This has been fixed in the latest release of funcotator and the data sources.

If you grab the latest software and the latest data sources release this problem should go away.

Sorry for the inconvenience.

chatchawit commented 6 years ago

I've tried the latest GATK today. The error message changed. Please help. Thanks.

Using GATK jar /omics/chatchawit/gatk2/gatk-package-4.0.4.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /omics/chatchawit/gatk2/gatk-package-4.0.4.0-local.jar Funcotator -R /omics/chatchawit/bundle/hsa38.fasta -V /omics/chatchawit/sm/out/sample21.vcf -O /omics/chatchawit/sm/anno/sample21.vcf --output-file-format VCF --data-sources-path /omics/chatchawit/bundle/dsrc/ --ref-version hg38 10:24:13.971 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/omics/chatchawit/gatk2/gatk-package-4.0.4.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 10:24:14.182 INFO Funcotator - ------------------------------------------------------------ 10:24:14.183 INFO Funcotator - The Genome Analysis Toolkit (GATK) v4.0.4.0-0.0.2 10:24:14.183 INFO Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/ 10:24:14.183 INFO Funcotator - Executing as chatchawit@omics on Linux v3.13.0-133-generic amd64 10:24:14.184 INFO Funcotator - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_161-b12 10:24:14.184 INFO Funcotator - Start Date/Time: April 28, 2018 10:24:13 AM ICT 10:24:14.184 INFO Funcotator - ------------------------------------------------------------ 10:24:14.184 INFO Funcotator - ------------------------------------------------------------ 10:24:14.185 INFO Funcotator - HTSJDK Version: 2.14.3 10:24:14.185 INFO Funcotator - Picard Version: 2.18.2 10:24:14.186 INFO Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2 10:24:14.186 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 10:24:14.186 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 10:24:14.186 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 10:24:14.186 INFO Funcotator - Deflater: IntelDeflater 10:24:14.186 INFO Funcotator - Inflater: IntelInflater 10:24:14.186 INFO Funcotator - GCS max retries/reopens: 20 10:24:14.186 INFO Funcotator - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 10:24:14.187 WARN Funcotator -

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Warning: Funcotator is a BETA tool and is not yet ready for use in production

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

10:24:14.187 INFO Funcotator - Initializing engine 10:24:15.574 INFO FeatureManager - Using codec VCFCodec to read file file:///omics/chatchawit/sm/out/sample21.vcf 10:24:15.701 INFO Funcotator - Done initializing engine log4j:WARN No appenders could be found for logger (org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils). log4j:WARN Please initialize the log4j system properly. log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info. 10:24:15.728 INFO FeatureManager - Using codec VCFCodec to read file file:///omics/chatchawit/bundle/dsrc/dbsnp/hg38/hg38_All_20170710.vcf.gz 10:24:15.884 INFO FeatureManager - Using codec XsvLocatableTableCodec to read file file:///omics/chatchawit/bundle/dsrc/oreganno/hg38/oreganno.tsv 10:24:15.945 INFO FeatureManager - Using codec GencodeGtfCodec to read file file:///omics/chatchawit/bundle/dsrc/gencode/hg38/gencode.v27.chr_patch_hapl_scaff.annotation.REORDERED.gtf WARNING 2018-04-28 10:24:17 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream 10:24:29.369 INFO ProgressMeter - Starting traversal 10:24:29.370 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 10:24:36.192 INFO Funcotator - Shutting down engine [April 28, 2018 10:24:36 AM ICT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.37 minutes. Runtime.totalMemory()=5195694080 java.lang.StringIndexOutOfBoundsException: String index out of range: -2 at java.lang.String.substring(String.java:1967) at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createUtrFuncotation(GencodeFuncotationFactory.java:1088) at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createGencodeFuncotationOnTranscript(GencodeFuncotationFactory.java:601) at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createFuncotationsHelper(GencodeFuncotationFactory.java:529) at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createFuncotationsOnVariant(GencodeFuncotationFactory.java:276) at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.createFuncotations(DataSourceFuncotationFactory.java:137) at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.createFuncotations(DataSourceFuncotationFactory.java:113) at org.broadinstitute.hellbender.tools.funcotator.Funcotator.enqueueAndHandleVariant(Funcotator.java:496) at org.broadinstitute.hellbender.tools.funcotator.Funcotator.apply(Funcotator.java:387) at org.broadinstitute.hellbender.engine.VariantWalkerBase.lambda$traverse$0(VariantWalkerBase.java:110) at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184) at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175) at java.util.Iterator.forEachRemaining(Iterator.java:116) at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801) at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481) at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471) at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151) at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174) at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418) at org.broadinstitute.hellbender.engine.VariantWalkerBase.traverse(VariantWalkerBase.java:108) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:892) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:134) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:179) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:198) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289)

jonn-smith commented 6 years ago

@chatchawit Interesting. Just double-checking, did you also get the latest data sources for Funcotator?

chatchawit commented 6 years ago

I've checked the README file (see below). I think it's the latest one because I cannot see the newer version in the ftp site.

Funcotator was able to produce some output. So I tried Funcotator with the same VCF input but with only first 5 loci. The program terminated safely.

I hypothesized that the bug happened with only some records in the VCF file which was produced from Mutect2.

Please help.

+---------------------------------------------+ | Data Source Version Information | +---------------------------------------------+

Version: 1.2.20180329 Source: ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/funcotator/funcotator_dataSources.v1.2.20180 329.tar.gz Alternate Source: gs://broad-public-datasets/funcotator/funcotator_dataSources.v1.2.20180329.tar.gz

jonn-smith commented 6 years ago

@chatchawit You're correct - you have the latest version. I just wanted to double-check.

I think your intuition is correct about it only happening for certain variants. Are you able to share your file somehow? I can see where it's happening but having some variants that cause the issue would be helpful to debug.

chatchawit commented 6 years ago

I gave the two lines that caused the error. By removing these lines in VCF input, the program was able to proceed to the next. There was the next line that caused the error. Unfortunately, I did not know how many lines. Note that VCF input was produced from Mutect2.

Complete VCF: https://drive.google.com/open?id=1UOUTtnNwVpBzTlJ9SPukon9aSHGOqJfW

chr1 959248 . A AAGAT . . DP=111;ECNT=4;POP_AF=0.016;P_GERMLINE=-8.838e-03;TLOD=3.19 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:107,2:0.027:31,2:76,0:16:186,156:40:1:0.00,0.020,0.018:0.073,1.660e-03,0.925

chr1 1273803 . G GCGC . . DP=12;ECNT=1;IN_PON;POP_AF=0.016;P_GERMLINE=-1.931e-05;RPA=5,6;RU=CGC;STR;TLOD=6.39 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:7,2:0.291:4,2:3,0:37:188,211:42:44:0.192,0.192,0.222:0.023,0.021,0.956

jonn-smith commented 6 years ago

OK, great. I'll run these and try to get to the bottom of this.

chatchawit commented 6 years ago

Should I wait for a bug fix ? Can I do something to avoid the error? Thanks.

jonn-smith commented 6 years ago

Unfortunately this is going to need a code fix. I should be able to get to it by early next week.

jonn-smith commented 6 years ago

Quick update - this bug occurs when handling alternate alleles (I believe of size > 1 base) in 5' UTRs.

I'm working on a fix now.

chatchawit commented 6 years ago

image

I guess you've done something. How can I know that the bug has been fixed? How to download and install the new version? Please help. Thank you.

jonn-smith commented 6 years ago

@chatchawit I just merged the code into master, so it should be live now.

If you build the GATK from source you will get the latest update - do you need help doing this?

chatchawit commented 6 years ago

@jonn-smith I have sucessfully built GATK by these commands.

git clone https://github.com/broadinstitute/gatk gradlew bundle

I've got this zip file in folder "build". gatk-4.0.4.0-34-g2cc7abd-SNAPSHOT.zip

So I unzipped and used this to replace GATK-4.0.4.0 that I downloaded from https://github.com/broadinstitute/gatk/releases/download/4.0.4.0/gatk-4.0.4.0.zip.

I still found errors.

21:09:33.811 INFO ProgressMeter - Starting traversal 21:09:33.811 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 21:09:46.267 INFO ProgressMeter - chr1:24929636 0.2 3000 14453.2 21:09:59.072 INFO ProgressMeter - chr1:64681324 0.4 6000 14251.2 21:10:09.456 INFO ProgressMeter - chr1:156245393 0.6 9000 15149.8 21:10:21.510 INFO ProgressMeter - chr1:206965947 0.8 12000 15094.7 21:10:26.132 INFO Funcotator - Shutting down engine [May 23, 2018 9:10:26 PM ICT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 1.36 minutes. Runtime.totalMemory()=11500781568 java.lang.IllegalArgumentException: Genomic positions must be > 0. at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:722)

What should I do? Can you send me one that is ready-to-use? Thanks.

jonn-smith commented 6 years ago

@chatchawit - That looks right to me.

I'll look into it. Can you send the full stack trace? This is probably a different issue and may be related to one I'm working on now.

chatchawit commented 6 years ago

Please find the stack trace below. Hopefully helpful.

Using GATK jar /omics/chatchawit/gatk3/gatk-package-4.0.4.0-34-g2cc7abd-SNAPSHOT-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /omics/chatchawit/gatk3/gatk-package-4.0.4.0-34-g2cc7abd-SNAPSHOT-local.jar Funcotator -R /omics/chatchawit/bundle/hsa38.fasta -V /omics/chatchawit/sm/out/test.vcf -O /omics/chatchawit/sm/anno/test.vcf --output-file-format VCF --data-sources-path /omics/chatchawit/bundle/dsrc/ --ref-version hg38 23:24:49.725 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/omics/chatchawit/gatk3/gatk-package-4.0.4.0-34-g2cc7abd-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_compression.so 23:24:49.934 INFO Funcotator - ------------------------------------------------------------ 23:24:49.934 INFO Funcotator - The Genome Analysis Toolkit (GATK) v4.0.4.0-34-g2cc7abd-SNAPSHOT-0.0.3 23:24:49.934 INFO Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/ 23:24:49.935 INFO Funcotator - Executing as chatchawit@omics on Linux v3.13.0-133-generic amd64 23:24:49.935 INFO Funcotator - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_161-b12 23:24:49.935 INFO Funcotator - Start Date/Time: May 23, 2018 11:24:49 PM ICT 23:24:49.935 INFO Funcotator - ------------------------------------------------------------ 23:24:49.935 INFO Funcotator - ------------------------------------------------------------ 23:24:49.936 INFO Funcotator - HTSJDK Version: 2.15.0 23:24:49.936 INFO Funcotator - Picard Version: 2.18.2 23:24:49.936 INFO Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2 23:24:49.936 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 23:24:49.936 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 23:24:49.936 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 23:24:49.937 INFO Funcotator - Deflater: IntelDeflater 23:24:49.937 INFO Funcotator - Inflater: IntelInflater 23:24:49.937 INFO Funcotator - GCS max retries/reopens: 20 23:24:49.937 INFO Funcotator - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 23:24:49.937 WARN Funcotator -

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Warning: Funcotator is a BETA tool and is not yet ready for use in production

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

23:24:49.937 INFO Funcotator - Initializing engine 23:24:51.025 INFO FeatureManager - Using codec VCFCodec to read file file:///omics/chatchawit/sm/out/test.vcf 23:24:51.169 INFO Funcotator - Done initializing engine log4j:WARN No appenders could be found for logger (org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils). log4j:WARN Please initialize the log4j system properly. log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info. 23:24:51.204 INFO FeatureManager - Using codec VCFCodec to read file file:///omics/chatchawit/bundle/dsrc/dbsnp/hg38/hg38_All_20170710.vcf.gz 23:24:51.451 INFO FeatureManager - Using codec XsvLocatableTableCodec to read file file:///omics/chatchawit/bundle/dsrc/oreganno/hg38/oreganno.tsv 23:24:51.535 INFO FeatureManager - Using codec GencodeGtfCodec to read file file:///omics/chatchawit/bundle/dsrc/gencode/hg38/gencode.v27.chr_patch_hapl_scaff.annotation.REORDERED.gtf WARNING 2018-05-23 23:24:53 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream 23:25:09.380 INFO ProgressMeter - Starting traversal 23:25:09.381 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 23:25:20.674 INFO ProgressMeter - chr1:24929636 0.2 3000 15941.9 23:25:42.601 INFO ProgressMeter - chr1:64681324 0.6 6000 10837.2 23:25:54.659 INFO ProgressMeter - chr1:156245393 0.8 9000 11926.3 23:26:06.846 INFO ProgressMeter - chr1:206965947 1.0 12000 12529.6 23:26:12.318 INFO Funcotator - Shutting down engine [May 23, 2018 11:26:12 PM ICT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 1.38 minutes. Runtime.totalMemory()=10974920704 java.lang.IllegalArgumentException: Genomic positions must be > 0. at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:722) at org.broadinstitute.hellbender.utils.param.ParamUtils.isPositive(ParamUtils.java:153) at org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils.getAlignedPosition(FuncotatorUtils.java:336) at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createSequenceComparison(GencodeFuncotationFactory.java:1392) at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createCodingRegionFuncotationForProteinCodingFeature(GencodeFuncotationFactory.java:751) at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createExonFuncotation(GencodeFuncotationFactory.java:649) at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createGencodeFuncotationOnTranscript(GencodeFuncotationFactory.java:609) at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createFuncotationsHelper(GencodeFuncotationFactory.java:541) at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createFuncotationsOnVariant(GencodeFuncotationFactory.java:288) at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.createFuncotations(DataSourceFuncotationFactory.java:137) at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.createFuncotations(DataSourceFuncotationFactory.java:113) at org.broadinstitute.hellbender.tools.funcotator.Funcotator.enqueueAndHandleVariant(Funcotator.java:496) at org.broadinstitute.hellbender.tools.funcotator.Funcotator.apply(Funcotator.java:387) at org.broadinstitute.hellbender.engine.VariantWalkerBase.lambda$traverse$0(VariantWalkerBase.java:110) at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184) at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175) at java.util.Iterator.forEachRemaining(Iterator.java:116) at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801) at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481) at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471) at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151) at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174) at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418) at org.broadinstitute.hellbender.engine.VariantWalkerBase.traverse(VariantWalkerBase.java:108) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:918) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:134) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:179) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:198) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289)

jonn-smith commented 6 years ago

@chatchawit Thanks. From the stack trace it looks like another issue that I'm actually currently working on. I'm not sure when it will be done, but I'm going through it as part of fixing #4739 (it's an aggravating bug that will require some refactoring).

jonn-smith commented 6 years ago

@chatchawit If you haven't already, try again with the latest release. It should help. There are also updated Data Sources in the usual place.

jonn-smith commented 6 years ago

@chatchawit Is this still an issue?

chatchawit commented 6 years ago

Hi John,

The last time (a couple months ago) I were not able to run the Funcotator with my data. I've already switched to Oncotator and almost finish the project.

Best,

Chatchawit A.

From: Jonn Smith notifications@github.com Sent: Wednesday, August 29, 2018 12:57 AM To: broadinstitute/gatk Cc: Chatchawit Aporntewan; Mention Subject: Re: [broadinstitute/gatk] java.lang.IllegalArgumentException: Invalid interval. (#4712)

@chatchawithttps://github.com/chatchawit Is this still an issue?

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