Work 120912

2015-01-13

azim58 - 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.

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