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Issues list

poppunk_visualise unable to find sequence in clustering question Further information is requested
#313 by fgonzalez3 was closed Jun 9, 2024
2
Unable to create the group "/sketches/": (Links) Object already exists
#308 by danielarothschild was closed Mar 23, 2024
2
Listeria monocytogenes database is missing graph file.
#300 by DOH-JDJ0303 was closed Feb 26, 2024
7
Generating jaccard distances per kmer
#284 by JLC2141 was closed Oct 5, 2023
3
PackagesNotFoundError
#283 by RoyUnderwoodAbramski was closed Sep 20, 2023
2
What to expect for a sample that may have a mixture of two or more strains
#281 by ilyavs was closed Aug 29, 2023
2
extract genome assemblies from database
#280 by reaset41 was closed Aug 24, 2023
1
IndexError: list index out of range (running current master branch) when running poppunk_assign
#273 by HarryHung was closed Nov 30, 2023
25
databases: reference only vs all genomes
#269 by sapuizait was closed Nov 30, 2023
1
Incorrect merge reporting from novel queries step bug Something isn't working
#268 by johnlees was closed Jun 19, 2023
@johnlees
1
[database] A double-checked database of Neisseria meningitidis enhancement New feature or request
#267 by tanzhizhou was closed Feb 26, 2024
@johnlees
8
visualize only query?
#266 by reaset41 was closed Nov 30, 2023
1
--write-references option when running PopPUNK assign
#265 by avrilcoghlan was closed Nov 30, 2023
2
Retreive source sequences from a database
#264 by phisanti was closed May 5, 2023
1
Popunk installed with conda cannot import scikit-learn's KernelDensity
#263 by sapoudel was closed Apr 21, 2023
Unmatched parentheses in newick tree
#260 by drhoads was closed Apr 14, 2023
12
Query data not working
#258 by Drojok was closed Apr 14, 2023
10
Increase maxIter with mandrake, and also add option
#255 by johnlees was closed Apr 14, 2023
1
Wrong DB for E. coli
#254 by jpaganini was closed Feb 3, 2023
2
Can't download Enterococcus faecium databases
#253 by martinmchugh was closed Jan 19, 2023
2
Running Poppunk v2.5.0 with --multi-boundry --> OverflowError
#248 by avonm was closed Nov 30, 2023
8
Clustering may not be reproducible with some large data sets
#247 by stitam was closed Nov 30, 2023
5
Allow update DB with QC failures code Changes to the coding implementation enhancement New feature or request
#243 by johnlees was closed Nov 17, 2022
1
@johnlees
AttributeError: module 'pp_sketchlib' has no attribute 'sparsifyDists' bug Something isn't working package Packaging of code
#241 by drhoads was closed Nov 17, 2022
3
issue with recent joblib update
#238 by jts1044 was closed Oct 31, 2022
1
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