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 program will stop.

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

Installing Pbindex

Probably the easiest way to install pbindex is described in PacBio & Bioconda. The instructions are basically:

  1. Install conda (see installing conda),

  2. Setup the channels (as described in bioconda channels), and

  3. 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 for details).

Using Pbindex from sm-analysis

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

/home/david/.venvs/pdp

and let us assume that pbbioconda was installed in:

/home/david/miniconda3

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

source /home/david/.venvs/pdp/bin/activate

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

sm-analysis --pbindex-path /home/david/miniconda3/bin/pbindex