Hi, TEAM
I use the AnalyzeCovariates of GATK but I got some error information about Rscript.
my code is following:
/hwfssz1/ST_HEALTH/Population_Genomics/User/dangningxin/bin/java/jre1.8.0_144/bin/java -jar /hwfssz1/ST_HEALTH/Population_Genomics/User/xuwenhao/software/GenomeAnalysisTK.jar -T AnalyzeCovariates -R /hwfssz1/ST_HEALTH/Population_Genomics/User/xuwenhao/data/refer/reference_human_hg38/hg38.fa -before hg38.recal.08-1.grp -after hg38.recal.08-2-pic.grp -plots hg38.recal.grp.09.pdf -csv hg38.recal.grp.09.csv &
And I got the error in the following:
> INFO 15:32:03,797 HelpFormatter - ----------------------------------------------------------------------------------
> INFO 15:32:03,801 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
> INFO 15:32:03,801 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
> INFO 15:32:03,801 HelpFormatter - [Tue Sep 05 15:32:03 CST 2017] Executing on Linux 2.6.32-696.el6.x86_64 amd64
> INFO 15:32:03,802 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_144-b01
> INFO 15:32:03,811 HelpFormatter - Program Args: -T AnalyzeCovariates -R /hwfssz1/ST_HEALTH/Population_Genomics/User/xuwenhao/data/refer/reference_human_hg38/hg38.fa -before hg38.recal.08-1.grp -after hg38.recal.08-2-pic.grp -plots hg38.recal.grp.09.pdf -csv hg38.recal.grp.09.csv
> INFO 15:32:03,828 HelpFormatter - Executing as xuwenhao@login-25-2.local on Linux 2.6.32-696.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_144-b01.
> INFO 15:32:03,828 HelpFormatter - Date/Time: 2017/09/05 15:32:03
> INFO 15:32:03,829 HelpFormatter - ----------------------------------------------------------------------------------
> INFO 15:32:03,829 HelpFormatter - ----------------------------------------------------------------------------------
> ERROR StatusLogger Unable to create class org.apache.logging.log4j.core.impl.Log4jContextFactory specified in jar:file:/hwfssz1/ST_HEALTH/Population_Genomics/User/xuwenhao/software/GenomeAnalysisTK.jar!/META-INF/log4j-provider.properties
> ERROR StatusLogger Log4j2 could not find a logging implementation. Please add log4j-core to the classpath. Using SimpleLogger to log to the console...
> INFO 15:32:03,978 GenomeAnalysisEngine - Deflater: JdkDeflater
> INFO 15:32:03,979 GenomeAnalysisEngine - Inflater: JdkInflater
> INFO 15:32:03,982 GenomeAnalysisEngine - Strictness is SILENT
> INFO 15:32:04,335 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
> INFO 15:32:04,518 GenomeAnalysisEngine - Preparing for traversal
> INFO 15:32:04,529 GenomeAnalysisEngine - Done preparing for traversal
> INFO 15:32:04,529 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
> INFO 15:32:04,530 ProgressMeter - | processed | time | per 1M | | total | remaining
> INFO 15:32:04,530 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
> INFO 15:32:04,713 ContextCovariate - Context sizes: base substitution model 2, indel substitution model 3
> INFO 15:32:04,869 ContextCovariate - Context sizes: base substitution model 2, indel substitution model 3
> INFO 15:32:04,882 AnalyzeCovariates - Generating csv file 'hg38.recal.grp.09.csv'
> INFO 15:32:05,056 AnalyzeCovariates - Generating plots file 'hg38.recal.grp.09.pdf'
> ##### ERROR --
> ##### ERROR stack trace
> org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Unable to start command: Rscript -e tempLibDir = '/tmp/Rlib.6366373699030600185';source('/tmp/BQSR.583089656080371624.R'); /hwfssz1/ST_HEALTH/Population_Genomics/User/xuwenhao/realut/test/hg38.recal.grp.09.csv /hwfssz1/ST_HEALTH/Population_Genomics/User/xuwenhao/realut/test/hg38.recal.08-1.grp /hwfssz1/ST_HEALTH/Population_Genomics/User/xuwenhao/realut/test/hg38.recal.grp.09.pdf
> Reason: Cannot run program "Rscript": error=5, Input/output error
> at org.broadinstitute.gatk.utils.runtime.ProcessController.exec(ProcessController.java:173)
> at org.broadinstitute.gatk.utils.R.RScriptExecutor.exec(RScriptExecutor.java:170)
> at org.broadinstitute.gatk.engine.recalibration.RecalUtils.generatePlots(RecalUtils.java:555)
> at org.broadinstitute.gatk.tools.walkers.bqsr.AnalyzeCovariates.generatePlots(AnalyzeCovariates.java:373)
> at org.broadinstitute.gatk.tools.walkers.bqsr.AnalyzeCovariates.initialize(AnalyzeCovariates.java:387)
> at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83)
> at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:323)
> at org.broad-bash: INFO: command not found
I'm confused why the Rscript can't run.And I check my Rscript
which Rscript
/hwfssz1/ST_HEALTH/Immune_And_Health_Lab/Public_Software/R/R-3.4.1/bin/Rscript