Entering edit mode
3.5 years ago
smrutimayipanda
▴
20
I am facing an error while running GATK Basecalibrator.
[1 July 2021 at 5:00:42 PM IST] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 35.00 minutes.
Runtime.totalMemory()=791674880
htsjdk.samtools.SAMFormatException: Did not inflate expected amount
at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:147)
at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:96)
at htsjdk.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:550)
at htsjdk.samtools.util.BlockCompressedInputStream.processNextBlock(BlockCompressedInputStream.java:532)
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.read(BlockCompressedInputStream.java:241)
at htsjdk.tribble.readers.TabixReader.readLine(TabixReader.java:215)
at htsjdk.tribble.readers.TabixReader.access$300(TabixReader.java:48)
at htsjdk.tribble.readers.TabixReader$IteratorImpl.next(TabixReader.java:434)
at htsjdk.tribble.readers.TabixIteratorLineReader.readLine(TabixIteratorLineReader.java:46)
at htsjdk.tribble.TabixFeatureReader$FeatureIterator.readNextRecord(TabixFeatureReader.java:170)
at htsjdk.tribble.TabixFeatureReader$FeatureIterator.<init>(TabixFeatureReader.java:159)
at htsjdk.tribble.TabixFeatureReader.query(TabixFeatureReader.java:133)
at org.broadinstitute.hellbender.engine.FeatureDataSource.refillQueryCache(FeatureDataSource.java:569)
at org.broadinstitute.hellbender.engine.FeatureDataSource.queryAndPrefetch(FeatureDataSource.java:538)
at org.broadinstitute.hellbender.engine.FeatureManager.getFeatures(FeatureManager.java:352)
at org.broadinstitute.hellbender.engine.FeatureContext.getValues(FeatureContext.java:173)
at org.broadinstitute.hellbender.engine.FeatureContext.getValues(FeatureContext.java:125)
at org.broadinstitute.hellbender.engine.FeatureContext.getValues(FeatureContext.java:263)
at org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator.apply(BaseRecalibrator.java:189)
at org.broadinstitute.hellbender.engine.ReadWalker.lambda$traverse$0(ReadWalker.java:96)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:195)
at java.base/java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:177)
at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:195)
at java.base/java.util.Iterator.forEachRemaining(Iterator.java:133)
at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474)
at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.base/java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:497)
at org.broadinstitute.hellbender.engine.ReadWalker.traverse(ReadWalker.java:94)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1058)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
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)
What does this mean? Is it related to memory? My system has 16 GB memory, still it is giving me this error again and again. What to do to get rid of this?
what was the command line ? what is the output of the command
file /path/to/file.gzwith all your files with a.gzextension ? what is the output of the commandgunzip -t /path/to/file.gzwith all your files with a.gzextension ?with this error, I didn tget any output, so there is no question of output in .gz extension. My command line is: java -jar ../../gatk-4.2.0.0/gatk-package-4.2.0.0-local.jar BaseRecalibrator --input sort_Dup_aligned_reads_gatk.bam --known-sites ../../Common_database/GRCh37_latest_dbSNP_all.vcf.gz --output base_recall.table --reference ../../Common_database/GRCh37_latest_genomic.fna
it is a problem with your inputs
I am again facing issue while running gatk HaplotypeCaller.
Earlier also, I am getting the same issue with BaseRecalibrator which was raised in this thread. Can anyone please tell me whats the error about? I re-installed java but still didnt get any output.
So both of these problems remain unresolved?
You should post in the GATK forum for help for a specific response. Someone may still answer here.
GenoMax both the errors are same, related to java. I just want to know what this error is about?
Pierre already told you above that the error is with your input files. Something appears to be wrong with the compression of those files.
... and I asked you for the output of
gunzip -t /path/to/file.gz....I got this: gzip: no_chr_dbsnp.vcf.gz: invalid compressed data--crc error
gzip: no_chr_dbsnp.vcf.gz: invalid compressed data--length error
Hi, Pierre! I encountered the same error in the step of HaplotypeCaller. Which file do you mean? In my case, my output is vcf WITHOUT .gz. But I still got this error.
Hi, smrutimayipanda. Did you solved the problem? I'm working on WGS analysis of a pedigree of three individuals using GATK 4.2.0.0. I encountered exactly the same error in the step of generating gvcf file from bam file.
It was interesting that everything went on well for the first individual; I got gvcf file containing information of all the chromosomes for him. However, for the other two of the individuals, I encountered the error [htsjdk.samtools.SAMFormatException: Did not inflate expected amount] in processing chr6 and chr11, respectively.
You have met this error twice in BaseRecalibrator and HaplotypeCaller. Have you solved the one in BaseRecalibrator?
No I was not able to solve that. I used another pipeline for variant calling.
I contacted with the GATK team. They asked me to try using jdk-inflater and jdk-deflater, but the problem was not solved yet. Which pipeline you've changed to?
freebayes pipeline
Thanks for the information. I think I 'd better shift to that, too.