I have a script that is running in the normal-tumor pair mode. It seems to be running fine but stopped after running into issues in a specific region, which is 1_KN196472v1_fix:111106-133486. I tried to debug but am not sure what is the problem. I am not sure if this is a problem with the BAM files or the Fasta file. Can you help resolve this?
This is the error log:
Critical exception occurs on region: 1_KN196472v1_fix:111106-133486, program will be stopped.
com.astrazeneca.vardict.exception.RegionBoundariesException: The region 1_KN196472v1_fix:109906-0 is wrong. We have problem while reading it, possible the start is after the end of the region or the fasta doesn't contain this region.
at com.astrazeneca.vardict.data.ReferenceResource.retrieveSubSeq(ReferenceResource.java:60)
at com.astrazeneca.vardict.data.ReferenceResource.getReference(ReferenceResource.java:94)
at com.astrazeneca.vardict.data.ReferenceResource.getReference(ReferenceResource.java:74)
at com.astrazeneca.vardict.modes.AbstractMode.tryToGetReference(AbstractMode.java:153)
at com.astrazeneca.vardict.modes.SomaticMode.notParallel(SomaticMode.java:48)
at com.astrazeneca.vardict.VarDictLauncher.start(VarDictLauncher.java:65)
at com.astrazeneca.vardict.Main.main(Main.java:15)
Caused by: htsjdk.samtools.SAMException: Malformed query; start point 109906 lies after end point 0
at htsjdk.samtools.reference.AbstractIndexedFastaSequenceFile.getSubsequenceAt(AbstractIndexedFastaSequenceFile.java:175)
at htsjdk.samtools.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:49)
at com.astrazeneca.vardict.data.ReferenceResource.retrieveSubSeq(ReferenceResource.java:53)
... 6 more
Hello,
I have a script that is running in the normal-tumor pair mode. It seems to be running fine but stopped after running into issues in a specific region, which is 1_KN196472v1_fix:111106-133486. I tried to debug but am not sure what is the problem. I am not sure if this is a problem with the BAM files or the Fasta file. Can you help resolve this?
This is the error log:
Critical exception occurs on region: 1_KN196472v1_fix:111106-133486, program will be stopped. com.astrazeneca.vardict.exception.RegionBoundariesException: The region 1_KN196472v1_fix:109906-0 is wrong. We have problem while reading it, possible the start is after the end of the region or the fasta doesn't contain this region. at com.astrazeneca.vardict.data.ReferenceResource.retrieveSubSeq(ReferenceResource.java:60) at com.astrazeneca.vardict.data.ReferenceResource.getReference(ReferenceResource.java:94) at com.astrazeneca.vardict.data.ReferenceResource.getReference(ReferenceResource.java:74) at com.astrazeneca.vardict.modes.AbstractMode.tryToGetReference(AbstractMode.java:153) at com.astrazeneca.vardict.modes.SomaticMode.notParallel(SomaticMode.java:48) at com.astrazeneca.vardict.VarDictLauncher.start(VarDictLauncher.java:65) at com.astrazeneca.vardict.Main.main(Main.java:15) Caused by: htsjdk.samtools.SAMException: Malformed query; start point 109906 lies after end point 0 at htsjdk.samtools.reference.AbstractIndexedFastaSequenceFile.getSubsequenceAt(AbstractIndexedFastaSequenceFile.java:175) at htsjdk.samtools.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:49) at com.astrazeneca.vardict.data.ReferenceResource.retrieveSubSeq(ReferenceResource.java:53) ... 6 more
Thanks!