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Unable to locate file from biallelicGenotyper in jointer #305

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ggittu opened this issue Oct 8, 2018 · 0 comments
Open

Unable to locate file from biallelicGenotyper in jointer #305

ggittu opened this issue Oct 8, 2018 · 0 comments

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@ggittu
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ggittu commented Oct 8, 2018

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

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