Invalid taxon labels causes division by zero during parse run

[pierrebarbera]

Example invalid taxon name:
OTU_3747;56074372f84154d24af41b68ba2370a5f931dd4d;size=39546_2

Thrown error during parsing phase of pargenes:

  Average number of taxa: 182
  Max number of taxa: 1481
  Average number of sites: 0
  Max number of sites: 0
[Error] <type 'exceptions.ZeroDivisionError'> integer division or modulo by zero

[lucaslima1618]

Hi,
I tried every possibility of taxon labeling, but the same error appears.

[Error] <type 'exceptions.ZeroDivisionError'> integer division or modulo by zero
Writing report file in /home/lucaslima/Documentos/Output8/report.txt
When reporting the issue, please always send us this file.

May you please help me?

Thanks in advance.

The report.txt follows

report.txt

[BenoitMorel]

Hi Lucas,

Thanks for your report!

The report file says that ParGenes cannot find a file that should be installed by the installation script (install.sh in the top directory). Did you run this script before running ParGenes? If yes, could you please run it again and send me its output?

I will add a more explicit error message for this kind of issue :-)

Benoit

[lucaslima1618]

Hi Benoit,

Thanks a lot for you help. You were right. I had a unnoted problem with the install.sh.

When I execute it the follow error apears:

Could NOT find BISON (missing: BISON_EXECUTABLE)
-- Could NOT find FLEX (missing: FLEX_EXECUTABLE)
CMake Error at libs/pll-modules/libs/libpll/src/CMakeLists.txt:19 (BISON_TARGET):
Unknown CMake command "BISON_TARGET".

-- Configuring incomplete, errors occurred!
See also "/home/lucaslima/ParGenes/raxml-ng/build/CMakeFiles/CMakeOutput.log".
See also "/home/lucaslima/ParGenes/raxml-ng/build/CMakeFiles/CMakeError.log".

The log files in attachment.

Cheers,

CMakeError.log
CMakeOutput.log

[BenoitMorel]

It looks like you have some missing dependencies (flex and bison). See raxml-ng instructions to install them: https://github.com/amkozlov/raxml-ng#installation-instructions

If it still does not work, the best would be to directly ask in our raxml-ng google group: https://groups.google.com/forum/#!forum/raxml

Cheers,
Benoit

[BenoitMorel]

Hi Pierre,

after 6 months of procrastination, I fixed this. I don't think I can really detect wrong taxon names from ParGenes (raxml-ng would have to do it), but I replaced the very obscure error message with something less confusing ;-)