In order to perform the Gene Set Enrichment Analysis for many clusters of genes in batch processing,I try to use command line interface of GOAL (The GOAL is user-friendly in graphical user interface (GUI),but it also contains command line interface for batch processing. GOAL can be downloaded from website: http://bioinfo.iit.nrc.ca/GOAL/index.html), but I fail in parameters design of command line interface.It always shows an error in running when I use command line interface of GOAL , the GOAL parameters are as follows :
java -Xms32m -Xmx1024m -Xss10m -Djava.security.policy=server.policy -jar GOAL.jar --input-file="1998.txt" --output-dir="c:\333" --background-file="sgd.txt" --species="Saccharomyces cerevisiae" --hierarchy="All" --correction="Bonferroni" --maxParental=3 --minRoot=3 --pvalue=0.05D --minGenes=3
the error is as follows：
GOAnalysis... Error During Annotation Parsing java.lang.StringIndexOutOfBoundsException: String index out of range: 0 Error During Gene Grouping java.lang.NullPointerException Correction or gene count invalid, skipping further analysis. Done
the files “1998.txt" and "sgd.txt" are in the directory of GOAL software. How to fix this error? Or can you give an example to demonstrate the use of command line interface of GOAL，Or can you help me recommend another software for Gene Set Enrichment Analysis in batch processing. Thank you！
it seems to be an error in one of the input files. Try with a smaller file and see if you still get the error. Are there any blank lines in the file? The script may also be sensitive to tabulation and spaces - see if the error goes away after converting all tabulations to spaces and vice-versa.
Dear Giovanni M Dall'Olio,I try it again according to your suggestion, It still shows the error