Mark Wilson

Came up with one solution in #1225 but it needs some discussion

I ran it again and called it directly from one of the SMRT-Analysis directories as: ``` smrtsuite/install/smrtsuite-fromsrc_3.0.2.170012/bundles/smrttools/install/smrttools-fromsrc_3.0.2.170012/smrtcmds/bin/variantCaller ``` This still caused the same error. This points to: ``` smrtsuite/install/smrtsuite-fromsrc_3.0.2.170012/bundles/smrttools/install/smrttools-fromsrc_3.0.2.170012/private/pacbio/pythonpkgs/GenomicConsensus/binwrap/variantCaller ```...

Shouldn't the GenomicConsensus v2.0.0 variantCaller be correct as well though?

This was pulled from the `4-quiver/*F/cns_*F.sh` where `$PB_RUN` is the root of the PacBio run. ``` ($HOME/venv/falcon/bin/smrtcmds/variantCaller -x 5 -X 120 -q 20 -j 24 \ -r $PB_RUN/4-quiver/000001F_003/000001F_003_ref.fa aln-000001F_003.bam \...

As described above, from the command line I'm running version 2.0.0 of variantCaller and from the smrtsuite cmds I'm running version 1.1.0: ``` $ variantCaller --version 2.0.0 $ quiver --version...

I will reinstall FALCON-unzip tomorrow in a new virtualenv and see if that fixes things. Perhaps I've added some things to the $PATH that I'm not aware of.

I am rerunning from a fresh install. In the meantime, would it be possible for me to have access to a test bam and fa? I could try to compare...

I received the same error again. I spent quite a bit of time digging through the code to see where the file is validated. I couldn't seem to find the...