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Popgen error AttributeError: 'str' object has no attribute 'decode'

5

I run popgen following the [cookbook-popgen-sumstats.ipynb](https://github.com/dereneaton/ipyrad/blob/master/newdocs/API-analysis/cookbook-popgen-sumstats.ipynb) . Then the error occured. ``` In：popgen = Popgen(data=data, imap=imap) popgen.params Traceback (most recent call last): File "/home/mydjc/miniconda3/envs/ipyrad/lib/python3.10/site-packages/IPython/core/interactiveshell.py", line 3398, in run_code exec(code_obj, self.user_global_ns,...

mydjc

It seems at the moment that invoking ipyrad with the `--ipcluster` flag works great, but then it looks like it kills the engines and stops ipcluster after it finishes running....

isaacovercast

The [structure file format](https://www.ccg.unam.mx/~vinuesa/tlem09/docs/structure_doc.pdf) supports an optional 2nd column to indicate (with integer values) the a priori population from which each sample was obtained (e.g. sampling site). In ipyrad if...

isaacovercast

Looks like [fastq-dump will be deprecated](https://hpc.nih.gov/apps/sratoolkit.html), and the replacement (fasterq-dump) is better, so we should swap out or at least test for fasterq-dump _first_ and then maybe fall back to...

isaacovercast

denovo+reference/denovo-reference not supported in v0.9 (yet)

25

Hello, it looks like the hybrid assembly approach outlined in the documentation is not supported for the 'ddrad' datatype in v0.19 and v0.20 (as is removed from the params file...

leonardslog

window_extracter: 'str' object has no attribute 'decode'

1

This issue seems similar to #451, but since it's a different function, I figured I'd open another issue. I'm trying to subset my phylip from ipyrad to include less missing...

alexkrohn

Recover all sites (invariant sites) in vcf

6

Hello, Let me first thank you for this great tool. I was wondering if there is any way I could obtain all invariant sites that are actually covered by the...

biolevol

Chloroplast DNA problems

4

Hello I just finished the basic assembly and the files that were returned only identified 13/188 samples. I am not quite sure what to make of it but was wondering...

c-mccarron

Feature Request: Restarting Partway Through a Step

5

It would be really nice to be able to restart ipyrad from the middle of a step rather than having to restart the entire step. This is probably most important...

alexkrohn

Object 'quartets' does not exist

4

I've encountered an error when trying to restart a tetrad run that failed because the Jupyter notebook shut down/restarted. The full error is posted below, and occurs immediately after restarted...

alexkrohn