Work+120912

I just want to test a simple thing today. I know that if I only give the program the top 5 peptides that it can find the HEE and PQRE motifs. However, I want to see if the program can find the motifs if I give it all 108 SMC peptides.

I made sure to increase the memory with -Xmx1024M I had the program use the fasta here "C:\kurt\storage\DR\2012\12-9-12\mpa\108_peptides.fa" The text of the main class that was run at this time is here

The program eventually had an error

Exception in thread "main" java.lang.IndexOutOfBoundsException: Index: 508, Size: 508 at java.util.ArrayList.RangeCheck(Unknown Source) at java.util.ArrayList.get(Unknown Source) at Glam2_Handler.processGLAM2Output(Glam2_Handler.java:120) at Glam2_Handler.processGLAM2Output(Glam2_Handler.java:78) at Glam2_Handler.call_GLAM2_command(Glam2_Handler.java:73) at MotifPeptideAnalysis.generateAllMotifs(MotifPeptideAnalysis.java:200) at MotifPeptideAnalysis.run(MotifPeptideAnalysis.java:70) at MotifPeptideAnalysis.main(MotifPeptideAnalysis.java:30)

The log file reached this line -2012/12/10 21:08:01 Currently comparing sequence 26 and 56 of a list of 108.