Terry Jones

Error decoding data from vim command

14

I ran `vim` in `daudin` to see how it would go. All went well until I exited. ``` >>> vim Makefile Traceback (most recent call last): File "/home/terry/s/me/daudin/daudinlib/interaction.py", line 58,...

I only notice this when I exit back into `fish` and type `mv ` (on typing the space the command line jumps around slightly and it's hard to see what...

The warning and behaviour regarding illegal characters in taxa names could be improved

4

Hi all I just got this in the raxml-ng (version 0.7.0) output: ``` NOTE: Following symbols are not allowed in taxa names to ensure Newick compatibility: NOTE: " " (space),...

Add a --header option when --outfmt 6 is used

12

It would be useful if there was a `--header` (or similar name) that could be used when `--outfmt 6` is used. That would allow people to post-process DIAMOND format 6...

DNA SAM output

7

Hi again Benjamin. Today I git pulled down the latest & saw the `qqual` output specifier - thanks again! I'm wondering if you've considered supporting SAM output that has the...

npm install error related to fsevents

10

Following https://nextstrain.github.io/auspice/introduction/install#installing-from-source after the `git clone` & `cd auspice` steps, I get: ```sh $ npm install --global . npm WARN checkPermissions Missing write access to /1GB/ncov/auspice/node_modules/fsevents npm WARN optional SKIPPING...

I can't run the tests fully. Many things fail. I'll open a ticket for that so you can see the output I get.

Errors when running tests on Mac OS X

2

There are quite a few errors hit when running the tests on OS X: ``` .................E...EEEE....E..........E.....EEEEEEE..............................E........................estscan not available for this platform: darwin EEE.......... ====================================================================== ERROR: test_orf_annotator (test.test_annotation.AnnotationTest) It tests orf...

ZeroDivisionError in anneal.py

4

I'm not sure how this can happen, but I'm looking at it in my terminal output, so I can at least say that it did happen! ``` File "/home/terry/s/net/simanneal/simanneal/anneal.py", line...

full_qqual seems to have become an int (was a string)

2

Hi Benjamin Running diamond `2.1.8`, I just had some tests fail due to `full_qqual` coming back as an int not a string. Should line 102 in `output/blast_tab_format.cpp`: ``` { "full_qqual",...