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broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool
GNU General Public License v2.0
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trying to polish nanopore with illumina don't understand the error #133

Open Ayse1006 opened 3 years ago

Ayse1006 commented 3 years ago

Hello, I runned the following command :

java -Xmx64G -jar pilon-1.24.jar --genome nano.fasta --frags illumina.sorted.bam --changes --fix all

But the script end before with the following problem : 

    at org.broadinstitute.pilon.BamFile.validateSeqs(BamFile.scala:78)
    at org.broadinstitute.pilon.GenomeFile.$anonfun$processRegions$1(GenomeFile.scala:87)
    at org.broadinstitute.pilon.GenomeFile.$anonfun$processRegions$1$adapted(GenomeFile.scala:87)
    at scala.collection.immutable.List.foreach(List.scala:333)
    at org.broadinstitute.pilon.GenomeFile.processRegions(GenomeFile.scala:87)
    at org.broadinstitute.pilon.Pilon$.main(Pilon.scala:111)
    at org.broadinstitute.pilon.Pilon.main(Pilon.scala)

I don't really know why... I checked other issues but no answer yet. I also checkes my bam file and it seems correct. Any help would be appreciated.

DylanDSouzaInd commented 1 year ago

Hi Ayse. Did you find a solution to this? I have the faced the same issue and need assistance.

JWang52md commented 7 months ago

I have the same issue