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PacificBiosciences / pbbioconda

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
BSD 3-Clause Clear License
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isoseq correct is very sensitive for style of input #684

Closed chvandijk closed 1 month ago

chvandijk commented 2 months ago

Package name isoseq 4.0.0

Describe the bug While running this line of code, I receive the error message: isoseq correct –-barcodes ${barcodes} ${input} ${output}

Error message | 20240508 12:42:27.824 | FATAL | isoseq correct ERROR: [isoseqs] barcode correction option parsing ERROR: Barcode-set required.

Fix If I run it like this, it runs smoothly without any errors. All the file paths are exactly the same

isoseq correct --barcodes ${barcodes} \
--log-level DEBUG --log-file isoseq_correct.log \
${input} ${output}
armintoepfer commented 1 month ago

Sounds like a problem in your environment? Adding logging has not impact on the CLI parsing