Pbindex

The sm-analysis program delegates the indexing of one-molecule BAM files to pbindex, which must be accessible at runtime. By default, pbindex is searched for in the PATH. If it is not found in the PATH, you will receive an informative runtime error message:

[CRITICAL] [Errno 2] No such file or directory: 'pbindex'

and the sm-analysis program itself will stop.

In that case, the instructions in the following sections can help you.

Installing Pbindex

pbindex is provided by the pbbam package. A simple way to install pbbam is with conda. Have a look at Setting up Bioconda, and follow the instructions in there if you want to choose the conda route. Once those steps are followed, and the resulting conda environment is active, install pbbam:

$ conda install pbbam

Upon success, you will be able to pass the path to the pbindex executable to sm-analysis if needed (see below how).

Warning

Notice that, contrary to the suggestion given in PacBio & Bioconda, the explicit selection of the bioconda channel by means of the -c option of conda install (e.g., conda install -c bioconda ...) triggers a dependency error. DO NOT USE the -c bioconda option, just run conda install ... instead, as explained in the main text.

Note

An alternative way to install pbindex is through SMRT-link software server tool.

Using Pbindex from sm-analysis

Let us assume that PacBio Data Processing was installed inside a virtual environment located in:

/home/dave/.venvs/pdp

and let us assume that pbbam was installed in:

/home/dave/miniconda3

then, after activating the PacBio Data Processing’s virtual environment:

$ source /home/dave/.venvs/pdp/bin/activate

you can tell sm-analysis about pbindex by using a command line option (sm-analysis -p) as follows:

$ sm-analysis --pbindex-path /home/dave/miniconda3/bin/pbindex