franciscozorrilla metaGEM issues

franciscozorrilla / metaGEM

:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

https://franciscozorrilla.github.io/metaGEM/

MIT License

189 stars 41 forks source link

issues

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[Question]: Creating a community model for 6-7 species using pre-binned MAGs obtained from elsewhere

#169 shikidj16 opened 1 hour ago
0
[Question]: Feature name data type issues and workflow failures when processing "crossMapSeries" output files in the "binRefine" workflow

#168 YuXia0 closed 3 weeks ago
4
dir_util.py AttributeError: 'dict' object has no attribute 'add'

#167 phil622 closed 1 month ago
3
Update README.md

#166 franciscozorrilla closed 2 months ago
0
Create CODE_OF_CONDUCT.md

#165 franciscozorrilla closed 2 months ago
0
abundance | samtools view: failed to add PG line to the header

#164 kunaljaani opened 2 months ago
2
How to set media to interpret and compare the metabolic interactions at different habitats?

#163 CODRbio opened 3 months ago
5
Implementation of EukRep in the Snakemake pipeline

#162 Rachita-Kumar opened 3 months ago
4
crossmap with multiple threads

#161 kunaljaani closed 3 months ago
2
maintenance: check bonus tool implementation in Snakefile and wrapper

#160 franciscozorrilla opened 6 months ago
0
ERROR when using GTDBTK

#158 pwzation closed 6 months ago
2
[Bug]: Metawrap Installation failure

#154 Amit-H opened 8 months ago
5
bugfix: Update metaGEM.sh

#151 franciscozorrilla closed 8 months ago
0
[Question]: How to use the GEM output of CarveMe to generate these two files?

#149 microbial-cookie closed 8 months ago
1
Create CITATION.bib

#148 franciscozorrilla closed 8 months ago
0
Update README.md

#147 franciscozorrilla closed 8 months ago
0
[Question]: I meet some errors when I use CarveMe for gap-filling?

#146 microbial-cookie closed 8 months ago
3
[Question]:Why, when I use CarveMe for gap-filling, does it show that my custom medium does not exist in the database?

#145 microbial-cookie closed 9 months ago
1
[Question]: How to define and construct a custom culture medium component that can be recognized by CarveMe?

#144 microbial-cookie closed 9 months ago
2
refined_bins output remains empty after successful binRefine step

#143 kunaljaani closed 8 months ago
2
Getting the following error while running the bash metaGEM.sh -t check

#142 microbial-cookie closed 9 months ago
8
Getting the following error while running the bash metaGEM.sh -t check

#141 microbial-cookie closed 10 months ago
0
Questions about media, gapfilling, and predicting interactions

#139 Qing-microbiol closed 9 months ago
11
[Usage]: running workflow on workstation with local flag

#138 flefler closed 1 year ago
17
[Bug]: 'BiGG_gene' is both an index level and a column label, which is ambiguous.

#137 Baizhou12138 closed 1 year ago
4
Job submission with qsub

#136 fbartusch closed 1 year ago
2
CompositionVis & modelVis output

#135 SoleilSu closed 1 year ago
7
[Question]: Install on mac M2?

#134 transition-bio-1 closed 9 months ago
5
automate the response to y/n

#133 kunaljaani closed 11 months ago
6
Create test.md

#132 franciscozorrilla closed 1 year ago
0
Create issue template

#131 franciscozorrilla closed 1 year ago
0
feature: support single batch gtdbtk classification

#130 franciscozorrilla opened 1 year ago
0
feature: add support for eggnog-mapper

#129 franciscozorrilla opened 1 year ago
0
minor bugfix: crossMapParallel Snakefile rule

#128 codechenx closed 1 year ago
1
feature: subworkflow for isolate genomes

#127 franciscozorrilla opened 1 year ago
0
minor bugfix: maxbin Snakefile rule

#126 franciscozorrilla closed 1 year ago
0
low number of species after binning for metaGEM model reconstruction

#125 Zhaoju-Deng closed 1 year ago
2
improvement: use `wc` to count bp instead of summing contig header info for abundance

#124 franciscozorrilla opened 1 year ago
1
feature: test & enable bioconda installation on macbook

#123 franciscozorrilla opened 1 year ago
1
Installation error

#122 fconstancias closed 1 year ago
5
feature: add dead-end counter for assembly evaluation

#121 franciscozorrilla opened 1 year ago
0
Allow non-cluster instances to run in parallel

#120 Xentrics closed 1 year ago
3
feature: profile DNA damage to determine ancient or modern provenance

#119 franciscozorrilla opened 1 year ago
1
Error in GTDBK : for extractDnaBins command

#118 aksbiome closed 1 year ago
1
Error parsing number of cores (--cores, -c, -j): must be integer, empty, or 'all'.

#117 LiZhihua1982 closed 1 year ago
1
Run snakemakefile-no results

#116 LiZhihua1982 closed 1 year ago
8
Install Problem

#115 LiZhihua1982 closed 1 year ago
5
How to caculate the smetana result's significant difference

#114 jllhghf closed 1 year ago
2
Having difficulties understanding SMETANA codes

#113 White-Shinobi closed 1 year ago
1
Is SMETANA able to use a comprehensive medium which simulates the human gut?

#112 White-Shinobi closed 1 year ago
3