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Old 02-18-2018, 11:08 PM   #3
DrYak
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Location: South Africa

Join Date: Sep 2013
Posts: 12
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Quote:
Originally Posted by GenoMax View Post
Can you only try "-Xmx24052m threads=12" ? Don't use -Xms=.
Hi,

Thank you for the suggestion.

With the "-Xmx24052m threads=12" flag it runs with 12 threads and the memory but still has an ArrayIndexOutOfBoundsException in multiple threads...

Code:
Set threads to 12
Initial:
Memory: max=25224m, free=25194m, used=30m

Input is being processed as unpaired
Started output streams: 1.357 seconds.
Exception in thread "Thread-6" java.lang.ArrayIndexOutOfBoundsException: 39
        at structures.EntropyTracker.averageEntropy(EntropyTracker.java:302)
        at structures.EntropyTracker.passes(EntropyTracker.java:348)
        at jgi.BBDukF$ProcessThread.run(BBDukF.java:2583)
Exception in thread "Thread-9" java.lang.ArrayIndexOutOfBoundsException: 30
        at structures.EntropyTracker.averageEntropy(EntropyTracker.java:302)
        at structures.EntropyTracker.passes(EntropyTracker.java:348)
        at jgi.BBDukF$ProcessThread.run(BBDukF.java:2583)
Exception in thread "Thread-12" Exception in thread "Thread-7" java.lang.ArrayIndexOutOfBoundsException
java.lang.ArrayIndexOutOfBoundsException
Exception in thread "Thread-14" java.lang.ArrayIndexOutOfBoundsException
Exception in thread "Thread-15" java.lang.ArrayIndexOutOfBoundsException
Exception in thread "Thread-17" java.lang.ArrayIndexOutOfBoundsException
Exception in thread "Thread-11" java.lang.ArrayIndexOutOfBoundsException
Exception in thread "Thread-10" java.lang.ArrayIndexOutOfBoundsException
Exception in thread "Thread-8" java.lang.ArrayIndexOutOfBoundsException
Exception in thread "Thread-13" java.lang.ArrayIndexOutOfBoundsException
Exception in thread "Thread-16" java.lang.ArrayIndexOutOfBoundsException
Processing time:                1.649 seconds.

Input:                          19931 reads             1964689 bases.
Low entropy discards:           1237 reads (6.21%)      123216 bases (6.27%)
Total Removed:                  1249 reads (6.27%)      123686 bases (6.30%)
Result:                         18682 reads (93.73%)    1841003 bases (93.70%)

Time:                           3.658 seconds.
Reads Processed:       19931    5.45k reads/sec
Bases Processed:       1964k    0.54m bases/sec
Is it because there are so many low complexity reads? Are there any other ways of filtering these polyT tracks (they tend to have the 8bp barcode followed by polyT, for eg:

@D00278:496:CC4LRANXX:7:1109:7642:2397 1:N:0:1
AAGACGGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
+
BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF<FFFFFFFFFFFFFFFFFFFFFFFFFF

Thanks,
Dave
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