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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
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SMETANA error: smetana.py:104, Failed to find a solution for growth of ' + org_id
#111
White-Shinobi
closed
1 year ago
5
Composition Vis is summarising strangly
#110
Xentrics
closed
1 year ago
3
How could I get full name of compound in SMETANA result?
#109
HongxiangXu
closed
2 years ago
2
Run the workflow locally
#108
Poccia
closed
1 year ago
1
Error in running metaGEM.sh
#107
Poccia
opened
2 years ago
0
CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
#106
tan-yuwei
closed
2 years ago
3
megahit (or other executable) in a background mode
#105
paristzou
closed
2 years ago
2
conda metagem environment
#104
paristzou
closed
2 years ago
4
Error parsing number of cores (--cores, -c, -j): must be integer, empty, or 'all'.
#103
CynthiaChibani
closed
2 years ago
13
Question about using crossMapParallel
#102
yhbae6022
closed
1 year ago
10
binReassemble gets stop abruptly
#100
kunaljaani
closed
2 years ago
5
-h hours to allocated to job runtime
#99
kunaljaani
closed
2 years ago
2
Fix an issue with metabat2
#98
Xentrics
closed
2 years ago
0
Suggestion: Remove temporary output of CrossMapParallel
#97
Xentrics
closed
2 years ago
1
Fix assembly stat
#96
Xentrics
closed
2 years ago
1
Fix an error in kallisto2concut
#95
Xentrics
closed
2 years ago
2
Fix for conda issues in env_setup.sh script
#94
BartoszBartmanski
closed
2 years ago
1
feat: develop rules for SMETANA global metrics
#93
franciscozorrilla
closed
2 years ago
1
Questions from /r/bioinformatics
#92
franciscozorrilla
closed
2 years ago
0
Question about CarveMe, SMETANA media
#91
yhbae6022
closed
2 years ago
2
maintenance: check env installation recipes
#90
franciscozorrilla
closed
2 years ago
1
Add rules for Diamond (blastp) and Prodigal
#89
zoey-rw
closed
2 years ago
8
Question about applying method for different biomes
#88
sskashaf
closed
1 year ago
1
Regarding the result data counts in Zenodo for European women samples
#87
jckim012
closed
2 years ago
2
Errors in env_setup.sh
#86
yumyai
closed
1 year ago
1
other inputs
#85
smb20200615
closed
1 year ago
9
Regarding the generation of SMETANA's highly statistically significant difference for NGT/IGT/T2D
#84
jckim012
closed
2 years ago
5
error in organizing dataset folder into sample-specific folders
#83
zoey-rw
closed
2 years ago
2
No metabat/samplename/cov/*.all.depth file and an empty concoct coverage_table.tsv
#82
slambrechts
closed
1 year ago
1
docs: expand on the interpretation of SMETANA results
#81
franciscozorrilla
closed
2 years ago
1
refactor: modify crossMap/concoct rule inputs and outputs
#77
franciscozorrilla
closed
2 years ago
0
feature: test and compare new binners
#76
franciscozorrilla
opened
3 years ago
4
Feat: use scaffolding information for binning
#75
franciscozorrilla
closed
2 years ago
0
Error in rule binRefine (one of the commands exited with non-zero exit code)
#74
slambrechts
closed
1 year ago
13
-bash: snakemake: command not found when running binRefine
#73
slambrechts
closed
3 years ago
4
feat: replace bwa-mem with bwa-mem-2
#72
franciscozorrilla
closed
2 years ago
1
Error when running compositionVis task
#71
zpf0117b
closed
3 years ago
15
documentation: describe usage of --parallel flag in bin reassembly
#70
franciscozorrilla
closed
2 years ago
0
feat: re-introduce mOTUs2 into workflow
#69
franciscozorrilla
closed
2 years ago
0
feat: add drep for dereplicating MAGs across samples
#68
franciscozorrilla
closed
2 years ago
0
feat: add rules to create and query custom protein db using diamond
#67
franciscozorrilla
closed
2 years ago
0
MAG abundance across samples
#66
zoey-rw
closed
1 year ago
1
feat: add viral identification module
#65
franciscozorrilla
closed
2 years ago
0
Query about SMETANA 'detailed' mode runtimes and parallel processing
#64
shreyanshumale
closed
3 years ago
3
Any way to make the compositionVis.R or abundanceVis.R scripts to work?
#63
shreyanshumale
closed
3 years ago
2
troubleshooting: poor assembly/binning in complex samples
#62
zoey-rw
closed
1 year ago
3
feat: Add support for BGC/MGC prediction
#61
franciscozorrilla
closed
2 years ago
0
crossMapseries vs crossMapParallel
#60
slambrechts
closed
3 years ago
6
Continue or restart failed or incomplete tasks
#59
slambrechts
closed
3 years ago
5
How can I check jobs are being submitted to our cluster
#58
slambrechts
closed
3 years ago
12
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