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nhansen / SVanalyzer

Tools for the analysis of structural variation in genomes
http://svanalyzer.readthedocs.io/
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./Build test failure #6

Closed Mkddb closed 4 years ago

Mkddb commented 4 years ago

Thanks nhansen.. For creating such a useful tool.

I am getting this error during installation in the building step. when i enter this command.. ./Build test

i am receiving this message.. please check if this is an error. if it can be skipped or fixed.

t/1_load.t .. ok
t/2_call.t .. 1/16

Failed test 'blib/script/SVwiden vartype'

at t/2_call.t line 47.

''

doesn't match '(?^:REPTYPE=DUP)'

Failed test 'blib/script/SVwiden widensmall'

at t/2_call.t line 49.

''

doesn't match '(?^:REFWIDENED=1:842056-842090)'

t/2_call.t .. 14/16 # Looks like you failed 2 tests of 16. t/2_call.t .. Dubious, test returned 2 (wstat 512, 0x200) Failed 2/16 subtests

Test Summary Report

t/2_call.t (Wstat: 512 Tests: 16 Failed: 2) Failed tests: 5-6 Non-zero exit status: 2 Files=2, Tests=38, 6 wallclock secs ( 0.04 usr 0.01 sys + 4.84 cusr 0.70 csys = 5.59 CPU) Result: FAIL Failed 1/2 test programs. 2/38 subtests failed.

Thanks in advance.

nhansen commented 4 years ago

Thanks for letting me know about this. Can you post the contents of the file t/test2.out in your SVanalyzer directory?

Mkddb commented 4 years ago

Yes,

The content in file t/test2.out says.. Can't open t//nucmer.prefix.delta, No such file or directory

While, there is another file as "nucmer.prefix.err" which has the following content.. nucmer: error while loading shared libraries: libumdmummer.so.0: cannot open shared object file: No such file or directory

am i missing some paths or some files itself ?

nhansen commented 4 years ago

It looks to me like there's a problem with your nucmer installation, then. Solution is to find that shared library file. Until then, all tools in SVanalyzer should work except for SVwiden, which uses nucmer to find widened coordinates of variants.