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bigdatagenomics / avocado

A Variant Caller, Distributed. Apache 2 licensed.
http://bdgenomics.org/projects/avocado/
Apache License 2.0
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Unable to locate file from biallelicGenotyper in jointer #305

Open ggittu opened 5 years ago

ggittu commented 5 years ago

I am trying to use jointer for the Adam files generated from biallelicGenotyper,

./avocado-submit jointer hdfs:///GATKexp/*.adam hdfs:///GATKexp/combineavocadofrombillalic.vcf

but it complaint saying unable to locate the file

Command body threw exception: java.io.FileNotFoundException: Couldn't find any files matching hdfs:///GATKexp/.adam for the requested PathFilter 18/10/08 15:17:06 INFO Jointer: Overall Duration: 1.74 secs Exception in thread "main" java.io.FileNotFoundException: Couldn't find any files matching hdfs:///GATKexp/.adam for the requested PathFilter.

I am able to do the jointer with the gvcf files( generated using GATK )

./avocado-submit jointer -from_gvcf /gvcffileavocado/*.g.vcf /gvcffileavocado/combineavocado.vcf