Arkadiy-Garber FeGenie issues

Arkadiy-Garber / FeGenie

HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes

GNU Affero General Public License v3.0

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issues

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No protein sequence for Cyc2

#47 EvaP29 opened 1 week ago
2
running programm with reference database for blast searches throws error

#46 ckeuschn opened 1 week ago
1
geneSummary output protein sequence EMPTY

#45 ckeuschn closed 3 weeks ago
2
'Namespace' object has no attribute 'hbm'

#44 Sxxnwei opened 5 months ago
1
where was the data for protein DmkA obtained from？

#43 xdli009 opened 1 year ago
1
Use of ORFs

#42 STabuteau opened 1 year ago
2
About iron-sulfur proteins

#41 maocheng2020 opened 1 year ago
1
error depth = open("%s/%s.depth" % (outDirectory, cell)) | HELP PLS.

#40 DrRumble opened 1 year ago
1
Renamed contigs?

#39 JBuongio opened 1 year ago
4
geneSummary file

#38 JBuongio opened 2 years ago
3
Rewrite using a workflow manager (snakemake, nextflow)

#37 phiweger opened 2 years ago
0
Permission denied when moving files

#36 aidanfoo96 opened 2 years ago
3
false negatives?

#35 metalichen opened 2 years ago
3
Error in hclust(d = dist(x = fegenie.scaled))

#34 manik-123 opened 2 years ago
1
Heatmap has same values regardless of what inflation factor I use

#33 patrickmon38 opened 2 years ago
2
Error - ValueError: could not convert string to float: 'EMPTY'

#32 JBuongio opened 2 years ago
38
Why the FeGenie installed by conda and the FeGenie installed manually work very differently？

#31 xdli009 opened 2 years ago
8
DIAMOND Verification: local variable 'idxDict' referenced before assignment

#30 mwittep opened 2 years ago
5
Error "hmmsearch: not found ... local variable 'hmmout' referenced before assignment" while running FeGenie

#29 anapopov opened 3 years ago
5
Update docker instructions in README

#28 note closed 3 years ago
0
Regarding --all_results option

#27 ShailNair opened 3 years ago
2
Create LICENSE

#26 Arkadiy-Garber closed 3 years ago
0
Tagged release and license file

#25 npavlovikj opened 3 years ago
17
Unable to run FeGenie.py

#24 yue-clare-lou closed 3 years ago
2
Issue with Installation

#23 18AS closed 3 years ago
4
relative abundace?

#22 plant272 opened 3 years ago
1
Update FeGenie.py

#21 AstrobioMike closed 3 years ago
1
Error when cluster ORFs

#20 Rachael-16 opened 3 years ago
1
ValueError: could not convert string to float: 'EMPTY' in -bams option

#19 gabriellerocap closed 3 years ago
7
generate multiple output types and/or reuse intermediate files

#18 gabriellerocap closed 3 years ago
3
bam option looks for jgi_summarize_bam_contig_depths

#17 gabriellerocap closed 3 years ago
3
Easy install with conda didn't locate packages

#16 Rene-Hoover closed 3 years ago
3
Where to hmms/iron

#15 bkemish opened 3 years ago
1
Annotation collisions and confusion about HMM model names

#14 karoraw1 closed 3 years ago
2
ValueError: invalid literal for int() with base 10: 'protein'

#13 pdalcinmartins opened 4 years ago
3
FileNotFoundError on "Easy Installation (if you don't have Conda)"

#12 diegusleik opened 4 years ago
1
Undetermined error

#11 CLMonteil opened 4 years ago
1
How to use -bams for a coassembly of some metagenomes

#10 pdalcinmartins opened 4 years ago
4
IndexError during Final processing of output

#9 zreitz closed 4 years ago
2
Various refinements2

#8 note closed 4 years ago
0
An error with FeGenie installed without conda (hmm path problem)

#7 ilnamkang closed 4 years ago
5
Add Dockerfile for fegenie deps

#6 note closed 4 years ago
10
Docker

#5 note closed 4 years ago
1
Option to output prodigal nucleotide file?

#4 ngilber3 closed 4 years ago
3
'rm: cannot remove (...): Directory not empty' error?

#3 GeoMicroSoares closed 4 years ago
3
Normalized gene abundances in 'FeGenie-heatmap-data.csv'?

#2 Anto007 closed 4 years ago
2
mod

#1 AstrobioMike closed 5 years ago
0