Ecosyste.ms: Issues

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GitHub / grp-bork/gunc issues and pull requests

#48 - speed issue

Issue - State: open - Opened by wenhaoli-wenhaoli 13 days ago - 2 comments

#47 - GTDB v220

Issue - State: closed - Opened by sheaster 2 months ago - 3 comments

#46 - Low quality/low gene numbers faa input causes crash

Issue - State: open - Opened by cschu 5 months ago

#45 - Provide commands to create database file [Feature Request]

Issue - State: open - Opened by chrisgulvik 5 months ago - 4 comments

#44 - update databases which resolves #41 and resolves #43

Pull Request - State: open - Opened by chrisgulvik 5 months ago

#43 - Database update for gunc

Issue - State: open - Opened by quliping 11 months ago - 2 comments

#42 - GUNC diamond output filename

Issue - State: open - Opened by jsgounot 11 months ago - 1 comment

#41 - GUNC gene_counts.json file not found!

Issue - State: closed - Opened by kayobianco about 1 year ago - 5 comments

#40 - New GTDB database release

Issue - State: open - Opened by pavlohrab about 1 year ago - 3 comments

#39 - Use .items instead of .iteritems, which is deprecated in pandas from v1.5.0 onwards.

Pull Request - State: closed - Opened by tmaklin over 1 year ago - 1 comment

#38 - Threshold CSS values when dealing with genomes in reference database

Issue - State: closed - Opened by mgabriell1 over 1 year ago - 4 comments

#37 - Suppress deprecation warning from pandas

Issue - State: closed - Opened by nelsonruth11 over 1 year ago - 1 comment

#36 - --use_species_level is not a better choice？

Issue - State: closed - Opened by nashanghenzan almost 2 years ago - 5 comments

#35 - --use_species_level is not a better choice？

Issue - State: closed - Opened by nashanghenzan almost 2 years ago - 1 comment

#34 - Command 'diamond --version' returned non-zero exit status 132

Issue - State: closed - Opened by sigau almost 2 years ago - 3 comments

#33 - diamond error

Issue - State: closed - Opened by nashanghenzan almost 2 years ago - 4 comments

#32 - Incompatibility with pandas 2.0

Issue - State: closed - Opened by SilasK almost 2 years ago - 2 comments

#31 - Failed to run Diamond

Issue - State: closed - Opened by ahmedmagds almost 2 years ago - 4 comments

#30 - apply GUNC to a large dataset of MAGs

Issue - State: closed - Opened by PatoUru about 2 years ago - 1 comment

#29 - Faster start up

Pull Request - State: closed - Opened by luispedro about 2 years ago

#28 - NAN in the output result

Issue - State: closed - Opened by zoubohao over 2 years ago - 13 comments

#26 - Update database selection option in documentation

Pull Request - State: open - Opened by akiledal over 2 years ago

#25 - false positives

Issue - State: closed - Opened by jhcuarta over 2 years ago - 8 comments

#24 - panda KeyError: 'contig'

Issue - State: closed - Opened by TianyiChang almost 3 years ago - 5 comments

#22 - file_suffix flag

Issue - State: closed - Opened by Biofarmer almost 3 years ago - 24 comments

#21 - Include "class" and "order" in contig assignment output file.

Pull Request - State: closed - Opened by aaronmussig almost 3 years ago

#20 - Diamond parameters - max-target-seqs

Issue - State: closed - Opened by hjruscheweyh almost 3 years ago - 4 comments

#19 - **conda install** no longer finds **diamond=2.0.4**

Issue - State: closed - Opened by fullama about 3 years ago - 9 comments

#18 - installation failure using conda

Issue - State: closed - Opened by ay-amityadav about 3 years ago - 5 comments

#17 - Use of `zgrep` is not portable across the conda/biocontainer ecosystem

Issue - State: closed - Opened by jfy133 over 3 years ago - 5 comments

#16 - Compare gunc profiling with dbs progenomes and GTDB

Issue - State: closed - Opened by SilasK over 3 years ago - 4 comments

#15 - diamond looking for wrong faa file

Issue - State: closed - Opened by SheikGeomicro over 3 years ago - 7 comments

#14 - Identify contaminant contigs

Issue - State: closed - Opened by mw55309 over 3 years ago - 4 comments

#13 - Cant download the database

Issue - State: closed - Opened by thh32 over 3 years ago - 3 comments

#12 - Internal KeyError when processing externally generated gene calls

Issue - State: closed - Opened by jdwinkler-lanzatech over 3 years ago - 7 comments

#11 - Report potential contaminating contigs

Issue - State: closed - Opened by donovan-h-parks almost 4 years ago - 2 comments

#10 - Documentation error

Issue - State: closed - Opened by cerebis almost 4 years ago - 1 comment

#9 - import plotly.graph_objects

Pull Request - State: closed - Opened by Hocnonsense about 4 years ago - 1 comment

#8 - No genome2taxonomy_ref.tsv file

Issue - State: closed - Opened by smb20200615 about 4 years ago - 2 comments

#7 - Error downloading DB

Issue - State: closed - Opened by michoug about 4 years ago - 4 comments

#5 - installation errors

Issue - State: closed - Opened by hexaquo about 4 years ago - 3 comments

#4 - Gunc merge_checkm file specification

Issue - State: closed - Opened by bsiranosian about 4 years ago - 4 comments

#3 - availability of the artificial genomes dataset

Issue - State: closed - Opened by ChiaraVanni about 4 years ago - 4 comments

#2 - Info/suggestions

Issue - State: closed - Opened by deoliveira86 about 4 years ago - 2 comments
Labels: bug, documentation

#1 - Minor issue: Unhelpful error when trying to download db into non-existing directory.

Issue - State: closed - Opened by dspeth about 4 years ago - 2 comments