eam12

functionality of -b option alone?

1

I am trying to understand what the `-b` option does when it is not paired with the `-c` option. I am working with a 4,640,668 bp long alignment. - When...

OSError: [Errno 39] Directory not empty: '5_final_blast'

4

I'm using version 2.8.5 of chewBBACA (installed via Conda) and am encountering the following error when I run `chewBBACA.py CreateSchema`: > Performing final BLASTp... > [====================] 100% > Removed 2...

Lost tree definition after saving

1

I recently downloaded FigTree v1.4.2 onto my Mac and noticed a strange thing happening after I initially visualize a tree, save it, close the tree, and then open it back...

Thank you so much for creating GrapeTree! I've been successfully using the GrapeTree command line module for generating trees for several years with no problem...until now. For some reason, the...

not recognizing changes to parameters

2

I'm running metAMOS as a job submission (via PBS job script) to a computer cluster. However, _runPipeline_ always runs the default parameters, no matter what parameters I change. For example,...

Updating tree and clusters without complete rerun?

1

Hello, I'm really loving ReporTree. Thank you so much for creating this valuable tool! I am looking to identify genetic clusters from a very large set of Salmonella isolates (>25,000)...

RecursionError: maximum recursion depth exceeded while calling a Python object

1

Thanks so much for creating ReporTree! I'm attempting to process a **very** large dataset (~45,000 isolates) using a cgMLST matrix (from chewBBACA) with the `--analysis HC` flag. An error occurred...

numpy.linalg.LinAlgError: Eigenvalues did not converge

5

Thank you so much for creating Pyseer! I'm trying to run a mixed effects model on unitigs following your recommended best practices. I have successfully run Pyseer (version 1.3.12, installed...