kmer not in bloomfilter warnings in stdlog.txt

[wichne]

Hello,

I have a set of 122M sequences from a microbial metagenome that I am running through Xander. I ran build (k=45, min_count=5), find and search separately. The contig merge and clustering parameters were left at defaults.

When I ran 'search' (using the provided rplB reference), it halted after the 'merge' step because no contigs were merged. ("Read in 625 contigs, wrote out 0 merged contigs in 0.577s"). The stdlog.txt had over 49K "kmer not in bloomfilter" warnings. Only 1251 kmers reported scores and a true/false value. Is this an expected result?

Please advise. Thanks, Bill

[OrsonMM]

Hello Wichne

You can install all Xander without problems. I have problems installing Rdptools with classifier, KmerFilter and Xander-HMMs ... When a use ant -f built.xml
It give a error related with junit library. You can help me with these please. Or give me a tip.

[rdpstaffmsu]

Please git clone the whole RDPTools package following the directions in ( https://github.com/rdpstaff/RDPTools). Let me know if there is any problem.

Benli Chai RDP Staff

On Wed, Sep 7, 2016 at 5:03 PM, Orson notifications@github.com wrote:

Hello Wichne

You can install all Xander without problems. I have problems installing Rdptools with classifier, KmerFilter and Xander-HMMs ... When a use ant -f built.xml

It give a error related with junit library. You can help me with these please. Or give me a tip.

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[OrsonMM]

Hi Benli

I have the similar problem installing these tools

Framebot , Xander-HMM and KmerFilter

with junit library maybe.

-do-compile-test: [javac] Compiling 10 source files to /home/orson/RDPTools/Xander-HMMgs/build/test/classes [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.5 [javac] warning: [options] source value 1.5 is obsolete and will be removed in a future release [javac] warning: [options] target value 1.5 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] /home/orson/RDPTools/Xander-HMMgs/test/edu/msu/cme/rdp/graph/filter/BloomFilterTest.java:31: error: package org.junit does not exist [javac] import org.junit.Test; [javac] ^ [javac] /home/orson/RDPTools/Xander-HMMgs/test/edu/msu/cme/rdp/graph/filter/BloomFilterTest.java:32: error: package org.junit does not exist [javac] import static org.junit.Assert.; [javac] ^ [javac] /home/orson/RDPTools/Xander-HMMgs/test/edu/msu/cme/rdp/graph/filter/NextCodonTest.java:21: error: package org.junit does not exist [javac] import org.junit.; [javac] ^ [javac] /home/orson/RDPTools/Xander-HMMgs/test/edu/msu/cme/rdp/graph/filter/NextCodonTest.java:22: error: package org.junit does not exist [javac] import static org.junit.Assert.; [javac] ^ [javac] /home/orson/RDPTools/Xander-HMMgs/test/edu/msu/cme/rdp/graph/filter/PathHolderTest.java:23: error: package org.junit does not exist [javac] import org.junit.Test; [javac] ^ [javac] /home/orson/RDPTools/Xander-HMMgs/test/edu/msu/cme/rdp/graph/filter/PathHolderTest.java:24: error: package org.junit does not exist [javac] import static org.junit.Assert.; [javac] ^ [javac] /home/orson/RDPTools/Xander-HMMgs/test/edu/msu/cme/rdp/graph/filter/SearchTest.java:21: error: package org.junit does not exist [javac] import org.junit.Test;

I hope your help, please.

[gunturus]

ant -f build.xml jar You can't compile with ant -f build.xml