Work+101512

I will try to spend only 1 hr working on this today.

Previously my "log_for_adding_items_to_table.txt" only added about 300 items. At this time, there was an out of memory error. I'll need to look into this. Maybe there was simply a lot of other things going on in the computer at that time.

I will try running this part of the code with the item count starting from where the program left off which was at 321.

The program had this error right away.

Exception in thread "main" java.lang.OutOfMemoryError: Java heap space at java.util.Arrays.copyOfRange(Unknown Source) at java.lang.String. (Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at java.io.BufferedReader.readLine(Unknown Source) at UsefulTools.storeTextFiletoArrayList(UsefulTools.java:539) at Blastp_Handler.extractDataFromLargeFastaBlastResult(Blastp_Handler.java:258) at Blastp_Handler.addEValuesFromLargeFastaBlastOutputToTable(Blastp_Handler.java:415) at MotifPeptideAnalysis.run(MotifPeptideAnalysis.java:146) at MotifPeptideAnalysis.main(MotifPeptideAnalysis.java:29)

The program has a problem with this line

ArrayList lines = useful_tools.storeTextFiletoArrayList(filepath);

and can't even store the file to an array list

It is true that this file "S:\Research\Cancer_Eradication\Users\kwhittem\DR\2012\9-28-12\mpa\blast\blast_results\blast_res\blast_res_motif_group_0_b_blast_res_motif_group_1_br\blast_res_motif_group_0_321_b_blast_res_motif_group_1.txt"

is much larger than all of the others at 212,011 KB.

Perhaps I can solve the problem by increasing the amount of memory that Java uses.

went to run->run configurations->arguments->added -Xmx512M according to info here http://www.coderanch.com/t/384456/java/java/Increase-JVM-heap-size-eclipse

still ran out of memory

tried -Xmx1024M which seems to be working. I'll have to see if it eventually runs out of memory or not. If it does, maybe for now I should just skip the 321 large blast result, and move on to the other files.

Alright I'll just let the program run overnight now. When I come back, I should see if there are any errors in Eclipse, and copy these. I should check the log and see if it is complete and says "Data from large fasta file blast results have been added to table;" I can also check the table of blast results and see which item was reached.

The following intervals ran out of memory 12001-14000 (actually it looks like just 14000 is the only one missing) 6011-8000 18001-20000