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Old 02-27-2018, 07:15 AM   #1
sfh838t
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Location: Mountain Grove, MO, USA

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Default problems with BBmap/java

hi,
I am trying to use BBmap to dedupe illumina paired end reads. (tried fastuniq but can't get past the "error in open left file first_read_name" error)
command line I used:
dedupe.sh in1= reads1.fq in2= reads2.fq out= outreads.fq

output starts with
java -Djava.library.path=..../bbmap/jni/
-ea -Xmx77448m -Xms77448m
-cp ...../bbmap/current/
jgi.Dedupe in1= reads1.fq in2= reads.fq
executing jgi.Dedupe.jgi[list of input vars]

Dedupe version 36.92
Exception in thread "main" java.lang.NullPointerEception
at jgi.Dedupe.<init>(Dedupe.java:211)
at jgi.Dedupe.main(Dedupe.java:86)

it seems that input is assigned to vars as it should, and something is not in the location it is supposed to be found in?
my java version is up to date, but I should say that I still do not have a good grasp on PATH
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Old 02-27-2018, 08:34 AM   #2
HESmith
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Remove the spaces after the equals (=) signs and try again.
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Old 02-27-2018, 09:35 AM   #3
sfh838t
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Jeez, would have never suspected that! Don't know if it will run through to the end ok, but it is running! thanks you very much!
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Old 02-28-2018, 04:58 AM   #4
sfh838t
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Default BBmap not finishing

Removing the white space after the equal sign has started BBmap running, but it has been running now (or seems to be at least, there is activity in system monitor) for about 20 hours.
I had one message right at the start : Set AbsorbContainment to false because it is not currently supported for paired reads.

Is this normal? both the message and the runtime?
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Old 02-28-2018, 05:07 AM   #5
HESmith
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From the manual: "Pair Limitations: Dedupe supports paired reads, but it was not really designed for them. When processing paired reads, some parts of Dedupe are restricted to a single thread due to a complication that causes non-deterministic output. As such, processing paired reads is slower than unpaired reads. Also, pair support is limited to exact matches and overlaps, not containments."

'AbsorbContainments' is enabled by default. You have to disable ('=false') in the command line (which is exactly what the warning instructed you to do).
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Old 02-28-2018, 06:11 AM   #6
sfh838t
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Thanks again. I had not found the manual yet.
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