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NationalGenomicsInfrastructure / piper

A genomics pipeline build on top of the GATK Queue framework
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Piper fails after last update #15

Closed vezzi closed 10 years ago

vezzi commented 10 years ago

When running:

 WholeGenome.sh --xml_input pipelineSetup.xml

or, using the NGI_pipeline: 

 piper -S /proj/a2010002/software/piper_bin/qscripts/DNABestPracticeVariantCalling.scala --xml_input /proj/a2010002/nobackup/NGI/analysis_ready/G.Grigelioniene_14_01_UUSNP/G.Grigelioniene_14_01_UUSNP_setup.xml --global_config /proj/a2010002/software/piper/uppmax_global_config.xml --number_of_threads 16 --scatter_gather 23 -jobRunner Drmaa --job_walltime 345600 -run --alignment_and_qc

I get the following error:

Error: Could not find or load main class org.broadinstitute.sting.queue.QCommandLine
johandahlberg commented 10 years ago

I missed changing to the new namespace convention in the build file, so it was looking for the wrong (non-existent) application main class. This should be fixed by f9f32ae91733d53108ed54d5cfd8d2e671799502.