Errors occurred when running MergeSam

[bli25wisc]

Hi @florianerhard ,

I am trying to run gedi's pipeline for Price. I encountered an error when running MergeSam. Any suggestions on fixing it?

Thanks!

My command is

gedi -e MergeSam -D -t ~/tmp/./parameters/scripts/test.prio.csv -prio ~/tmp/./parameters/scripts/test.prio.oml -chrM -o test.cit

The errors are listed below:

An error occurred: Inappropriate call if not paired read java.lang.IllegalStateException: Inappropriate call if not paired read at htsjdk.samtools.SAMRecord.requireReadPaired(SAMRecord.java:866) at htsjdk.samtools.SAMRecord.getSecondOfPairFlag(SAMRecord.java:936) at gedi.region.bam.BamAlignedReadDataFactory.addVariations(BamAlignedReadDataFactory.java:331) at gedi.region.bam.BamAlignedReadDataFactory.addRecord(BamAlignedReadDataFactory.java:99) at gedi.region.bam.FactoryGenomicRegion.add(FactoryGenomicRegion.java:71) at gedi.bam.tools.SamToRegion.apply(SamToRegion.java:67) at gedi.bam.tools.SamToRegion.apply(SamToRegion.java:38) at gedi.util.FunctorUtils$MappedIterator.next(FunctorUtils.java:1110) at gedi.util.FunctorUtils$PeekIterator.hasNext(FunctorUtils.java:605) at gedi.util.FunctorUtils$FilteredIterator.lookAhead(FunctorUtils.java:1059) at gedi.util.FunctorUtils$FilteredIterator.hasNext(FunctorUtils.java:1048) at gedi.util.FunctorUtils$MergeIterator.insert(FunctorUtils.java:348) at gedi.util.FunctorUtils$MergeIterator.next(FunctorUtils.java:323) at gedi.util.FunctorUtils$PeekIterator.hasNext(FunctorUtils.java:605) at gedi.util.FunctorUtils$MappedIterator.hasNext(FunctorUtils.java:1106) at gedi.util.FunctorUtils$PeekIterator.hasNext(FunctorUtils.java:604) at gedi.util.FunctorUtils$FilteredIterator.lookAhead(FunctorUtils.java:1059) at gedi.util.FunctorUtils$FilteredIterator.hasNext(FunctorUtils.java:1048) at gedi.util.FunctorUtils$InitActionIterator.hasNext(FunctorUtils.java:647) at gedi.util.FunctorUtils$PeekIterator.hasNext(FunctorUtils.java:604) at gedi.util.FunctorUtils$SideEffectIterator.hasNext(FunctorUtils.java:678) at gedi.util.FunctorUtils$HasNextActionIterator.hasNext(FunctorUtils.java:767) at gedi.util.FunctorUtils$PeekIterator.hasNext(FunctorUtils.java:604) at gedi.util.FunctorUtils$MultiplexIterator.lookAhead(FunctorUtils.java:950) at gedi.util.FunctorUtils$MultiplexIterator.hasNext(FunctorUtils.java:933) at gedi.util.FunctorUtils$PeekIterator.hasNext(FunctorUtils.java:604) at gedi.util.FunctorUtils$MappedIterator.hasNext(FunctorUtils.java:1106) at gedi.util.FunctorUtils$PeekIterator.hasNext(FunctorUtils.java:604) at gedi.util.FunctorUtils$SideEffectIterator.hasNext(FunctorUtils.java:678) at gedi.util.FunctorUtils$DemultiplexIterator.lookAhead(FunctorUtils.java:106) at gedi.util.FunctorUtils$DemultiplexIterator.hasNext(FunctorUtils.java:90) at gedi.util.FunctorUtils$PeekIterator.hasNext(FunctorUtils.java:604) at gedi.util.FunctorUtils$ResortIterator.tryFillCollector(FunctorUtils.java:1023) at gedi.util.FunctorUtils$ResortIterator.hasNext(FunctorUtils.java:998) at gedi.util.FunctorUtils$InitActionIterator.hasNext(FunctorUtils.java:647) at gedi.util.FunctorUtils$PeekIterator.hasNext(FunctorUtils.java:604) at gedi.util.FunctorUtils$SideEffectIterator.hasNext(FunctorUtils.java:678) at gedi.util.FunctorUtils$HasNextActionIterator.hasNext(FunctorUtils.java:767) at gedi.util.FunctorUtils$PeekIterator.hasNext(FunctorUtils.java:604) at gedi.util.FunctorUtils$MultiplexIterator.lookAhead(FunctorUtils.java:946) at gedi.util.FunctorUtils$MultiplexIterator.hasNext(FunctorUtils.java:933) at gedi.util.FunctorUtils$PeekIterator.hasNext(FunctorUtils.java:604) at gedi.util.FunctorUtils$FilteredIterator.lookAhead(FunctorUtils.java:1059) at gedi.util.FunctorUtils$FilteredIterator.hasNext(FunctorUtils.java:1048) at gedi.util.FunctorUtils$PeekIterator.hasNext(FunctorUtils.java:604) at gedi.util.FunctorUtils$SideEffectIterator.hasNext(FunctorUtils.java:678) at gedi.centeredDiskIntervalTree.CenteredDiskIntervalTreeStorage.fill(CenteredDiskIntervalTreeStorage.java:293) at gedi.core.region.GenomicRegionStorage.fill(GenomicRegionStorage.java:182) at executables.MergeSam.start(MergeSam.java:295) at executables.MergeSam.main(MergeSam.java:84)

[florianerhard]

Dear Bo,

you have to give me more details. Could you post the content of the bash script containing the call to MergeSam? Which gedi version did you use?

Best, Florian

[bli25wisc]

@florianerhard ,

Sure thing. I compiled Price 1.0.1 from your source code.

Please see the bash scripts attached.

test.prio.oml.txt test.prio.csv.txt test.bash.txt start.bash.txt

[florianerhard]

Dear Bo,

for using the pipeline, could you use the most recent version from github? We updated htsjdk before 1.0.1 which causes this error. This is fixed in the current version!

Best, Florian