Problems installing CoVizu backend on an Ubuntu system

[ArtPoon]

@SandeepThokala please provide details on the operating system environment, depenency versions, etc. here

[SandeepThokala]

In Jesry the following version were installed

• python 3.10.9
• conda 23.1.0
• mpi4py 3.1.4
• minimap2 2.24-r1155-dirty
• treetime 0.10.0
• fasttree 2 2.1.11
• biopython 1.80
• scipy 1.7.3

environment.zip

[SandeepThokala]

The full error message after trying to run the pipeline on jesry:

Traceback (most recent call last):
  File "./covizu/batch.py", line 150, in <module>
    timetree, residuals = build_timetree(by_lineage, args, cb.callback)
  File "./covizu/covizu/utils/batch_utils.py", line 84, in build_timetree
    return covizu.treetime.parse_nexus(nexus_file, fasta)
  File "./covizu/covizu/treetime.py", line 161, in parse_nexus
    rmean = statistics.mean(rvals)
  File "./miniconda3/envs/venv/lib/python3.10/statistics.py", line 328, in mean
    raise StatisticsError('mean requires at least one data point')
statistics.StatisticsError: mean requires at least one data point

[GopiGugan]

• I created a conda environment using the attached environment file. Installed the same FastTree, treetime versions as described above.
• Installing treetime again fixed the issue

[GopiGugan]

The error @SandeepThokala was getting was because there were no date estimates in the timetree.nexus file

https://github.com/PoonLab/covizu/blob/7cf87ca2a882490cc93fb7144cd429e691e9fab9/covizu/treetime.py#L131-L146

@SandeepThokala can you please let me know how you installed treetime? I installed version 0.10.0 as well and its working fine.

[SandeepThokala]

We cloned the treetime github repo, and installed it with pip.

[ArtPoon]

Close as norepro for now