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jdidion / atropos

An NGS read trimming tool that is specific, sensitive, and speedy. (production)
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TypeError: Object of type 'ProgressBarType' is not JSON serializable #102

Closed plijnzaad closed 4 years ago

plijnzaad commented 4 years ago

When calling atropos as follows: 

atropos -a $adaptor \
       --progress none \
       --report-file report.json \
       --single-input $inputsam \
       --output-format sam \
       --log-level WARNING \
       --log-file foo/$atroposlog | ....

I get a half-complete json file and the error TypeError: Object of type 'ProgressBarType' is not JSON serializable (stderr is here: err.txt ). .txt and .yaml report formats seem to work fine. Pickle (report.pickle) also gives an error ( TypeError: write() argument must be str, not bytes )

jdidion commented 4 years ago

Fixed in develop - will be in release alpha6