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Help! I am getting “Unsupported …”!

If you encounter the error Unsupported chemistries found: (...) or unsupported sequencing chemistry combination, your ccs binaries do not support the used sequencing chemistry kit, from here on referred to as “chemistry”. This may be because we removed support of an older chemistry or your binary predates release of the used chemistry. This is unlikely to happen with ccs from SMRT Link installations, as SMRT Link is able to automatically update and install new chemistries. Thus, the easiest solution is to always use ccs from the SMRT Link version that shipped with the release of the sequencing chemistry kit.

Old chemistries: With ccs 4.0.0, we have removed support for the last RSII chemistry P6-C4. The only option is to downgrade ccs with conda install pbccs==3.4.

New chemistries: It might happen that your ccs version predates the sequencing chemistry kit. To fix this, install the latest version of ccs with conda update --all. If you are an early access user, follow the monkey patch tutorial.

Monkey patch ccs to support additional sequencing chemistry kits

Please create a directory that is used to inject new chemistry information into ccs:

mkdir -p /path/to/persistent/dir/
cd /path/to/persistent/dir/
export SMRT_CHEMISTRY_BUNDLE_DIR="${PWD}"
mkdir -p arrow

Execute the following step by step instructions to fix the error you are observing and afterwards proceed using ccs as you would normally do. Additional chemistry information is automatically loaded from the ${SMRT_CHEMISTRY_BUNDLE_DIR} environmental variable.

Error: “unsupported sequencing chemistry combination”

Please download the latest out-of-band chemistry.xml:

wget https://raw.githubusercontent.com/PacificBiosciences/pbcore/develop/pbcore/chemistry/resources/mapping.xml -O "${SMRT_CHEMISTRY_BUNDLE_DIR}"/chemistry.xml

Error: “Unsupported chemistries found: (…)”

Please get the latest consensus model .json from PacBio and copy it to:

cp /some/download/dir/model.json "${SMRT_CHEMISTRY_BUNDLE_DIR}"/arrow/