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nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline
http://funannotate.readthedocs.io
BSD 2-Clause "Simplified" License
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Funannotate check does not recognize samtools #970

Open dgslos opened 8 months ago

dgslos commented 8 months ago

The output of funannotate check shows: ERROR: samtools found but error running samtools ERROR: samtools not installed

However, samtools 1.13 is installed and working.

A quick test makes me suspect it has something to do with the UTF-8 coding of the stdout in the subprocess command of the check script. Maybe the problem is in the 'universal_newlines=True' argument. Can this be checked?

Cheers, Dieter

hyphaltip commented 8 months ago

can you provide more information on the operating system, version of python, version of funannotate you are testing. This tests and works on a variety of unix and osx machines