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baoxingsong / AnchorWave

Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation
MIT License
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Merge gVCF #74

Closed zhengluo-lz closed 3 months ago

zhengluo-lz commented 3 months ago

Hi, Dr. Song When I used the process you provided to generate VCF files, as described in GATK.md, I encountered the following issue when merging gVCF files from different individuals. Have you encountered this issue before, and how can it be resolved?

java.lang.NumberFormatException: For input string: "C"
        at java.base/java.lang.NumberFormatException.forInputString(NumberFormatException.java:67)
        at java.base/java.lang.Integer.parseInt(Integer.java:662)
        at java.base/java.lang.Integer.parseInt(Integer.java:778)
        at htsjdk.tribble.readers.TabixReader.getIntv(TabixReader.java:337)
        at htsjdk.tribble.readers.TabixReader$IteratorImpl.next(TabixReader.java:438)
        at htsjdk.tribble.readers.TabixIteratorLineReader.readLine(TabixIteratorLineReader.java:46)
        at htsjdk.tribble.TabixFeatureReader$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.tools.genomicsdb.GenomicsDBImport$1.query(GenomicsDBImport.java:1016)
        at org.genomicsdb.importer.GenomicsDBImporter.<init>(GenomicsDBImporter.java:151)
        at org.genomicsdb.importer.GenomicsDBImporter.lambda$iterateOverChromosomeIntervals$4(GenomicsDBImporter.java:714)
        at java.base/java.util.concurrent.CompletableFuture$AsyncSupply.run(CompletableFuture.java:1768)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
        at java.base/java.lang.Thread.run(Thread.java:1583)
baoxingsong commented 3 months ago

Hi,

I did not have this problem before. I am wondering if this problem is repeatable. If you rerun the process, could you get the same error message?

zhengluo-lz commented 3 months ago

Yes, I still encounter the same issue, and I use maize as well.

baoxingsong commented 3 months ago

Did you rerun the pipeline only for the GATK, or rerun everything from the very beginning? I guess this error might be due to some previous programs not finishing successfully.

zhengluo-lz commented 3 months ago

MAF and gVCF were generated successfully, and the program did not report any error.

zhengluo-lz commented 3 months ago

I found the cause of the problem. It might be because the MAFToGVCFPlugin module in the new version of Tassel automatically generates a tbi index, but this index seems to have issues. When I rebuilt the index using tabix, there were no errors.

zhengluo-lz commented 3 months ago

I will close this issue. Thank you！