Question: Ximmer running error
0
gravatar for S AR
3 months ago by
S AR50
Pakistan
S AR50 wrote:

Im running the CNV analysis on 14 BAM files 7 from tumor and 7 from its germline which is in a folder

/mnt/d/AKU/FTP/BAM/

I ran the following command to test the tool:

./ximmer -v -nosim -c /mnt/d/AKU/FTP/BAM/config.groovy -o results

This is my config.groovy file:

bam_files="/mnt/d/AKU/FTP/BAM/*.bam"
target_regions="/mnt/d/AKU/FTP/BAM/TruSeq_exome_targeted_regions.hg19.bed"
concurrency=20
callers {
    cn.MOPs {}
    exomedepth {}
        Conifer {}
}

After Running im getting the following error:

Configured verbose logging
Ximmer  [1]     INFO    |6:51:57 Configured verbose logging
Caught: groovy.lang.MissingMethodException: No signature of method: groovy.util.ConfigObject.MOPs() is applicable for argument types: (script1541573517941211209064$_run_closure1$_closure2) values: [script1541573517941211209064$_run_closure1$_closure2@4b34fff9]
Possible solutions: sort(), is(java.lang.Object), plus(java.util.Collection), plus(java.util.Map), wait(), size()
groovy.lang.MissingMethodException: No signature of method: groovy.util.ConfigObject.MOPs() is applicable for argument types: (script1541573517941211209064$_run_closure1$_closure2) values: [script1541573517941211209064$_run_closure1$_closure2@4b34fff9]
Possible solutions: sort(), is(java.lang.Object), plus(java.util.Collection), plus(java.util.Map), wait(), size()
        at script1541573517941211209064$_run_closure1.doCall(script1541573517941211209064.groovy:5)
        at script1541573517941211209064$_run_closure1.doCall(script1541573517941211209064.groovy)
        at script1541573517941211209064.run(script1541573517941211209064.groovy:4)
        at Ximmer.main(Ximmer.groovy:1266)

While installing XIMMER i was unable to install only xhmm but all other tools were successfully installed and probed with ximmer and i was also unable to solve the xhmm error which is:

In file included from sources/lib/MatrixDecomp.cpp:3:0:
./sources/include/VectorOnDisk.hpp: In instantiation of ‘HMM_PP::VectorOnDisk<dataType>::~VectorOnDisk() [with dataType = double]’:
sources/lib/MatrixDecomp.cpp:75:1:   required from here
./sources/include/VectorOnDisk.hpp:91:37: error: throw will always call terminate() [-Werror=terminate]
        throw new Exception(str.str());
                                     ^
./sources/include/VectorOnDisk.hpp:91:37: note: in C++11 destructors default to noexcept
cc1plus: all warnings being treated as errors
config_rules.Makefile:16: recipe for target 'build/lib/MatrixDecomp.o' failed
make[2]: *** [build/lib/MatrixDecomp.o] Error 1
make[2]: Leaving directory '/home/sark/ximmer/eval/pipeline/tools/xhmm/statgen-xhmm-cc14e528d909/sources/hmm++'
Makefile:126: recipe for target 'sources/hmm++/' failed
make[1]: *** [sources/hmm++/] Error 2
make[1]: Leaving directory '/home/sark/ximmer/eval/pipeline/tools/xhmm/statgen-xhmm-cc14e528d909'
Makefile:121: recipe for target 'all' failed
make: *** [all] Error 2

Can anybody help me with this?

Thanks.

R cnv ximmer java python • 170 views
ADD COMMENTlink modified 3 months ago • written 3 months ago by S AR50
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