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dnaase / Bis-tools

A collection of tools to deal with Bisulfite-seq/NOMe-seq (SNP/Methylation calling: BisSNP; HMM segmentation: DMNTools; Visualization/Clustering: alignWigToBed; )
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Problem when running BisulfiteGenotyper #5

Open LiyanJi-code opened 5 years ago

LiyanJi-code commented 5 years ago

Hi, I'm running bis-snp when using the command: java -Xmx10G -jar BisSNP-1.0.1.jar -R hs37d5.fa -I header.sort.mdups.bam -D 00-All.vcf.gz -T BisulfiteGenotyper -vfn1 header.sort.mdups.cytosine.raw.vcf -vfn2 header.sort.mdups.snp.raw.vcf -C CG,1 -C CH,1 -out_modes EMIT_VARIANT_AND_CYTOSINES -stand_call_conf 10 -nt 12 -minConv 1 -vcfCache 1000000 -mmq 30 -mbq 5

But the following errors occur:

ERROR --

INFO 00:08:25,980 SAMDataSource$SAMReaders - Initializing SAMRecords in serial

ERROR stack trace

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:537) at htsjdk.samtools.util.BlockCompressedInputStream.processNextBlock(BlockCompressedInputStream.java:519) at htsjdk.samtools.util.BlockCompressedInputStream.nextBlock(BlockCompressedInputStream.java:455) at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:445) at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:194) at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:236) at htsjdk.tribble.readers.TabixReader.readLine(TabixReader.java:200) at htsjdk.tribble.readers.TabixReader$IteratorImpl.next(TabixReader.java:417) at htsjdk.tribble.readers.TabixIteratorLineReader.readLine(TabixIteratorLineReader.java:46) at htsjdk.tribble.TabixFeatureReader$FeatureIterator.readNextRecord(TabixFeatureReader.java:177) at htsjdk.tribble.TabixFeatureReader$FeatureIterator.next(TabixFeatureReader.java:215) at htsjdk.tribble.TabixFeatureReader$FeatureIterator.next(TabixFeatureReader.java:155) at org.broadinstitute.gatk.utils.refdata.utils.FeatureToGATKFeatureIterator.next(FeatureToGATKFeatureIterator.java:60) at org.broadinstitute.gatk.utils.refdata.utils.FeatureToGATKFeatureIterator.next(FeatureToGATKFeatureIterator.java:42) at org.broadinstitute.gatk.utils.iterators.PushbackIterator.next(PushbackIterator.java:65) at org.broadinstitute.gatk.utils.refdata.SeekableRODIterator.seekForward(SeekableRODIterator.java:356) at org.broadinstitute.gatk.engine.datasources.providers.ManagingReferenceOrderedView.getReferenceOrderedDataAtLocus(ManagingRe at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$MapDataIterator.next(TraverseLociNano.java:182) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$MapDataIterator.next(TraverseLociNano.java:153) at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:271) at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48) at org.broadinstitute.gatk.engine.executive.ShardTraverser.call(ShardTraverser.java:98) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.8-1-0-gf15c1c3ef):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions https://software.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Did not inflate expected amount
ERROR ------------------------------------------------------------------------------------------

Some of my bams passed through this process, while others failed. Any help would be much appreciated.

Thanks in advances.

LiyanJi-code commented 5 years ago

It turns out the problems with the header of input bams. The header of bams were modified with GATK AddOrReplaceReadGroups with the default parameters together with VALIDATION_STRINGENCY=LENIENT. The above problems were fixed.