VI. Troubleshooting

External packages issues

Issue: 'taxit' command crashes

This bug is related to the 'taxtastic' package, which is necessary to build pplacer 'reference packages'.

It may appear when a local installation of 'pip3' is conflicting with the 'pip3' encapsulated in Anaconda environments. Unexpected interactions between local and Anaconda pip packages are a known issue in Anaconda, in particular when different versions of the same package are installed in both contexts.

Solution:

1. Remove the taxtastic package from your local 'pip3' packages :

conda deactivate
pip3 uninstall taxtastic

2. Remove the taxtastic package from your conda 'pip3' installation :

conda activate PEWO
pip3 unistall taxtastic
pip3 install taxtastic

Issue: APPLES crashing during the Accuracy procedure

Crashes can be experienced with APPLES 1.2.4, in particular when short alignments are produced by the accuracy procedure.

#Crash example:

  File "miniconda3/envs/PEWO/bin/run_apples.py", line 48, in runquery
    jplace["placements"][0]["p"] = [alg.placement(criterion_name)]
  File "miniconda3/envs/PEWO/lib/python3.6/site-packages/apples/Algorithm.py", line 36, in placement
    placed_edge = min(valids, key=lambda e: self.error_per_edge(e))
ValueError: min() arg is an empty sequence

Recommendation from APPLES authors:

Change the threshold at line 7 on apples/distance.py file from 0.10 to 0.0005.

APPLES checks the size of the overlap between the query and a reference (i.e. # of sites where at least one of the two sequences in the pairwise alignment is not a gap character) and divides it by the size of the pairwise alignment. If it is lower than 0.1, the distance is set to -1, which means invalid. We put that threshold to ignore very fragmented queries. I think in your application you may want to lower that threshold or remove altogether.