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Old 06-04-2014, 12:54 AM   #60
punto_c
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Location: Japan, Tokyo

Join Date: Oct 2013
Posts: 11
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Hello Brian

I am trying to compare some mapping tools, and I am also using BBMap
I execute 4 tests using PE readed preprocessed with bbduck, cutadapt, fastx and trimmomatic respectively
With the reads preprocessed using bbduck and trimmomatic the program is able to finish without any error

When I run the reads preprocessed with cutadapt or fastx bbmap crashes...

do you have any idea why is this happening?

Here is the parameters I used and the stde output:
overwrite=true fastareadlen=500 -Xmx200g threads=96 outputunmapped=f sam=1.4

BBMap version 32.15
Set overwrite to true
Set threads to 96
Set DONT_OUTPUT_UNMAPPED_READS to true
Retaining first best site only for ambiguous mappings.
Set genome to 1

Loaded Reference: 9.674 seconds.
Loading index for chunk 1-7, build 1
Generated Index: 15.609 seconds.
Analyzed Index: 22.798 seconds.
Started output stream: 0.345 seconds.
Started output stream: 0.014 seconds.
Cleared Memory: 0.146 seconds.
Processing reads in paired-ended mode.
Started read stream.
Started 96 mapping threads.
Exception in thread "Thread-110" java.lang.IndexOutOfBoundsException: Index: 172, Size: 172
at java.util.ArrayList.rangeCheck(ArrayList.java:571)
at java.util.ArrayList.get(ArrayList.java:349)
at stream.ConcurrentGenericReadInputStream.pair(ConcurrentGenericReadInputStream.java:484)
at stream.ConcurrentGenericReadInputStream.readLists(ConcurrentGenericReadInputStream.java:361)
at stream.ConcurrentGenericReadInputStream.run(ConcurrentGenericReadInputStream.java:205)
at java.lang.Thread.run(Thread.java:679)
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