Task: progcheck

Task: progcheck

This checks that the external dependencies are found and that their versions are high enough.

Usage

The usage is:

circlator progcheck

(there are no options).

Output

Ideally, the output will look something like this:

Using bwa version 0.7.12 as /bin/bwa
Using nucmer version 3.1 as /bin/nucmer
Using prodigal version 2.60 as /bin/prodigal
Using samtools version 0.1.19 as /bin/samtools
Using spades version 3.5.0 as /bin/spades.py

Otherwise, there will be error messages. For example:

Version of bwa too low. I found 0.6.2, but must be at least 0.7.12. Found here:
/bin/bwa
Using nucmer version 3.1 as /bin/nucmer
Using prodigal version 2.60 as /bin/prodigal
Using samtools version 0.1.19 as /bin/samtools
Didn't find spades in path. Looked for:spades.py

In this case, Circlator was unable to find SPAdes in the user's path. It found BWA, but the version was too low. The remaining tools were OK.