mdmparis defense-finder issues

mdmparis / defense-finder

Systematic search of all known anti-phage systems.

GNU General Public License v3.0

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issues

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[BUG] miscalculation of alignment coverage

#68 jpjarnoux opened 2 weeks ago
0
[BUG]Issue with -A Option in DefenseFinder v3.1.0

#67 maocheng2020 opened 2 weeks ago
0
[BUG] Hmmer error

#66 mesti90 opened 2 weeks ago
1
[HELP] How do I know how many systems and subsystems are in the current DF?

#65 lianmsu opened 1 month ago
0
Add ADF and pandas posttreatment

#64 FlorianTesson closed 2 months ago
0
OSError: [Errno 39] Directory not empty: 'Cas'[BUG]

#63 chengzhongyi8 closed 3 weeks ago
1
Fix command for creating Conda environment

#62 memgonzales closed 4 months ago
0
`replicon` fused to `sys_id` in `defense_finder_genes` output

#61 ezherman closed 4 months ago
1
No way to change macsyfinder to linear topology from circular.

#60 chrisdoering8197 closed 1 month ago
1
Use pandas in the post treatment

#59 FlorianTesson closed 2 months ago
5
Allow to specify a path to an index dir for msf

#58 jeanrjc closed 5 months ago
1
macsyfinder:"No such model definition: 'defense-finder-models'"

#57 yaojian1997 closed 4 months ago
1
No such profile error in version 1.2.2

#56 roo-weed closed 4 months ago
1
What's the SOFIC system, we cannot find the reference article about this.

#55 liaohu1231 closed 6 months ago
2
sort lines before comparing them to improve test readability

#54 bryan-brancotte closed 7 months ago
1
Test more python versions

#53 bryan-brancotte closed 7 months ago
1
Alignment availability for RefSeq

#52 Ge0rges closed 6 months ago
2
Column header definitions and criteria for an HMM hit being listed in Systems or Genes tsv files

#51 asantia3 closed 5 months ago
1
use latest source from macsyfinder

#50 bryan-brancotte closed 7 months ago
1
Question of reduce the iops of shared-disk operations

#49 cron-weasley closed 5 months ago
1
Duplicated sequences while using pyrodigal when multiple FNA

#48 FlorianTesson closed 6 months ago
0
use tagged version not latest from sources

#47 bryan-brancotte closed 4 months ago
1
error when using unordered db-type

#46 schmittel closed 6 months ago
4
How to use Defensefinder for each draft genome or each MAG?

#45 actledge closed 4 months ago
2
AttributeError: 'NoneType' object has no attribute 'split'

#44 liucong2016 closed 2 months ago
3
Errno 39: Directory not empty: 'Cas'

#43 amorrod closed 4 months ago
2
macsypy.error.MacsypyError: 'defense-finder-models/Rst_Hydrolase-Tm__Hydrolase-Tm': No such profile

#42 ezherman closed 6 months ago
6
allow to force reinstall models

#41 bryan-brancotte closed 8 months ago
2
--db-type unordered is not processed correctly

#40 jeanrjc closed 2 weeks ago
6
Defense finder failed to run

#39 sujeetpowar closed 9 months ago
1
Inconsistencies between versions and local VS webserver results.

#38 TaraBartolec closed 4 months ago
3
Issue with defense_finder_posttreat for "aa" protein files

#37 rsheppar closed 9 months ago
2
macsyfinder: "No such model definition: 'CasFinder'"

#36 liaohu1231 closed 4 months ago
10
Draft: Add functional test

#35 bryan-brancotte closed 7 months ago
5
Command to update models

#34 rplanel closed 4 months ago
2
add possibility to run defensefinder on a nucleotide fasta

#33 jeanrjc closed 11 months ago
1
hmmsearch not honouring -w --workers

#32 tsp-kucbd closed 11 months ago
1
Feature msfv2 support

#31 bneron closed 1 year ago
0
an error occurred during Hmmer execution: command = hmmsearch

#30 davidmadariaga closed 1 year ago
1
AttributeError: 'DataFrame' object has no attribute 'append'. Did you mean: '_append'?

#29 joelwwh closed 4 months ago
3
webserver

#28 drp223 closed 6 months ago
1
Where are all bit score cutoffs reported? Missing for some systems in Liste_hmm_system.md

#27 scubalaina closed 4 months ago
2
Something wrong when I run until “Computing best solutions for UserReplicon ”

#26 gjzheng closed 6 months ago
3
request: add defense-finder to bioconda

#25 alexweisberg closed 11 months ago
2
defense-finder update error

#24 nayeon1994 closed 6 months ago
1
defense-finder update error: IndexError: list index out of range | issue downloading models

#23 scubalaina closed 6 months ago
5
Difference between number of HMM and Liste of hmm file

#22 jpjarnoux closed 6 months ago
1
IndexError: list index out of range when running 'defense-finder update'

#21 ZongzhiWu closed 6 months ago
2
Macsyfinder best_solution.tsv parsing error and suggested solution

#20 hsbi closed 6 months ago
3
FileNotFoundError: [Errno 2] No such file or directory: '/defense-finder-tmp/RM/best_solution.tsv' when using --db-type unordered

#19 felipehcoutinho closed 6 months ago
3