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MayurDivate / GUAVASourceCode

Source code repository for GUAVA (ATAC-seq data analysis tool).
GNU General Public License v3.0
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Exception in thread "main" java.lang.NullPointerException #26

Open deejdeej opened 4 years ago

deejdeej commented 4 years ago

When trying to run guava from the command line, we get:

$ guava.sh gdiff -n deejtest -o . -files testing.txt -g hg19

Exception in thread "main" java.lang.NullPointerException at umac.guava.diff.DifferentialOutputFiles.writeSummary(DifferentialOutputFiles.java:143) at umac.guava.diff.DifferentialAnalysisWorkflow.startCommandlineDifferentialAnalysis(DifferentialAnalysisWorkflow.java:148) at umac.guava.commandline.CommandlineWorkflow.prepareGdiffCommandlineWorkflow(CommandlineWorkflow.java:101) at umac.guava.commandline.CommandlineWorkflow.startCommandlineFlow(CommandlineWorkflow.java:38) at umac.guava.GUAVA.runGUAVAcommandline(GUAVA.java:83) at umac.guava.GUAVA.main(GUAVA.java:64)

$ cat testing.txt DMSO_Rep1_R1_aligned_ATACseq.bam

$ ls -la DMSO_Rep1_R1_aligned_ATACseq.bam -rw-rw-r-- 1 deej deej 274174803 Mar 4 15:33 DMSO_Rep1_R1_aligned_ATACseq.bam

$ java -version java version "1.8.0_191" Java(TM) SE Runtime Environment (build 1.8.0_191-b12) Java HotSpot(TM) 64-Bit Server VM (build 25.191-b12, mixed mode)

$ cat deejtest_GUAVA_Differental_analysis/deejtest_log.txt #######################################################

Project summary

Name of the project: deejtest

Genome build: hg19

Pvalue: 0.05

Foldchange: 2.0

Upstream: 5000

Downstream: 3000

Input files

Any thoughts on where to start looking?

Thank you