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

Probably the easiest way to install pbindex is with conda. Have a look at Setting up Bioconda. Once those steps are followed, and the resulting conda environment is active, install pbbam:

conda install -c bioconda pbbam

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

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 pbbioconda 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