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/test-data/gatk/gatk_analyze_covariates/gatk_analyze_covariates_out_1.log.contains

https://bitbucket.org/cistrome/cistrome-harvard/
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1Program Name: org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates
2Reading in input csv file...
3...Done!
4Writing out intermediate tables for R...
5Writing out data tables for read group: A Fake phiX Sample	with 340 observations	and aggregate residual error = -9.136
6...Done!
7Calling analysis R scripts and writing out figures...
8Analyzing read group: A Fake phiX Sample
9...Done!