Work 101512
2015-01-13azim58 - 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.<init>(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.ja
va: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\bl
ast_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