biobakery phylophlan issues

biobakery / phylophlan

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes

https://huttenhower.sph.harvard.edu/phylophlan

MIT License

128 stars 33 forks source link

issues

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Generate the same tree

#71 Biofarmer closed 3 years ago
2
Where are the bootstrap values in RAxML trees?

#70 liuyuwen1 opened 3 years ago
2
AttributeError: 'NoneType' object has no attribute 'replace'

#69 TonyMane opened 3 years ago
1
Discrepancy in the generated tree of life ?

#68 nlmjacquemin opened 3 years ago
5
examples run_*.sh :: typo in program names

#67 EricDeveaud opened 3 years ago
1
setup phylophlan for computer withoout network access

#66 EricDeveaud opened 3 years ago
9
Phylophlan searching for DIAMOND in anaconda, not miniconda3

#65 thh32 closed 3 years ago
2
[e] unable to download "http://cmprod1.cibio.unitn.it/databases/MetaRefSGB/releases/Sep20/SGB.Sep20.md5

#64 stephenqub opened 3 years ago
2
cannot run PhyloPhlAn with supermatrix_nt.cfg

#63 zhangws119 opened 3 years ago
1
phylophlan_strain_finder Error

#62 LisaCarraro closed 3 years ago
6
[e] expected str, bytes or os.PathLike object, not NoneType

#61 Virome1 opened 3 years ago
3
re-use database folder

#60 pxtm opened 3 years ago
5
phylophlan_write_config_file.py - can only concatenate str (not "tuple") to str

#59 cyklee closed 3 years ago
4
Heatmaps of the metagenomes --> mapping file?

#58 WebBach opened 3 years ago
1
The topology of the output trees

#57 MostafaYA closed 3 years ago
2
modify TMPDIR for mafft only if not present in env

#56 khillion closed 3 years ago
1
Improving merging function performances

#55 cumbof closed 3 years ago
1
[e] resolve_polytomies crashed

#54 myoreo777 opened 3 years ago
11
Phylophlan 2.0 release?

#53 richardsm32 opened 3 years ago
1
Problem at last step (gene refining) and --maas options

#52 pedrojcy91 opened 3 years ago
4
fix databases_folder error

#51 Hocnonsense closed 4 years ago
2
[e] unable to download "https://www.dropbox.com ... in phylophlan_metagenomic

#50 Hocnonsense closed 4 years ago
4
Any places could download the Built reference phylogeny

#49 444thLiao closed 3 years ago
1
Location of examples folder and database files

#48 KatariinaParnanen closed 3 years ago
1
[e] build_gene_tree crashed

#47 Hocnonsense closed 4 years ago
6
Problem with Example 01: S. aureus

#46 Shiqing-Nie closed 3 years ago
3
occured core dumped

#45 fujch7 closed 3 years ago
2
e] both db_dna and db_aa are None!

#44 Rob-murphys closed 3 years ago
4
This sequence may be truncated, or another sequence may be too long?

#43 zckoo007 closed 4 years ago
0
UnboundLocalError: local variable 'input_fna_clean' referenced before assignment

#42 fujch7 closed 3 years ago
5
Phylophlan_metagenomic.py

#41 wangjianing0618 closed 4 years ago
7
Documentation does not say how to download databases

#40 mw55309 closed 4 years ago
2
Both Nucleotide Databases Appear Empty

#39 JuliaMcGonigle closed 4 years ago
3
which tree should be used

#38 fujch7 closed 4 years ago
11
Is it possible to add eukaryotic core proteins to the PhyloPhlAn database?

#37 charlottecc closed 4 years ago
1
Fragmentary entries not accepted by RAxML

#36 TlaskalV closed 4 years ago
5
Phylophan_metagenomic's mash dist uses all cpus despite using --nproc

#35 jeanmanguy closed 4 years ago
2
gene_markers_identification crashed

#34 wqssf102 closed 4 years ago
4
/phylophlan_configs/" folder does not exists and unable to download phylophlan_databases.txt?dl=1

#33 zyyalice closed 3 years ago
23
Can not download the whole reference genomes.

#32 Lily-WL opened 4 years ago
4
local variable 'input_faa_clean' referenced before assignment

#31 Y-H-Joe closed 4 years ago
6
Python bang for serialize_matrix.py is wrong

#30 smoretti closed 4 years ago
1
Phylophlan_metagenomic.py : Problem to generate output files

#29 vindarbot opened 4 years ago
7
Minimum quality for including MAGs?

#28 adityabandla closed 4 years ago
1
gene_markers_selection crashed

#27 gunturus closed 4 years ago
13
Tree of life at nucleotide level

#26 gunturus closed 4 years ago
3
Tree of life for MetaPhlAn3 species

#25 alexhbnr closed 4 years ago
2
phylophlan_metagenomic, can not download database

#24 PandengWang closed 4 years ago
7
--subsample None?

#23 adityabandla closed 4 years ago
4
Default for --min_num_markers

#22 adityabandla closed 4 years ago
7

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