Ecosyste.ms: Issues

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GitHub / B-UMMI/chewBBACA issues and pull requests

#213 - Application of chewBBACA onto Fungal Genomes

Issue - State: open - Opened by maurkarr 15 days ago - 1 comment
Labels: Status: In Progress

#212 - PrepExternalSchema command stuck at 98% completeness

Issue - State: open - Opened by AnyaKovalenko 27 days ago - 5 comments
Labels: Status: In Progress

#211 - What will happen when using chewBBACA with a diploid genome?

Issue - State: open - Opened by dutchscientist about 1 month ago - 2 comments

#210 - Assigning cgSTs - Brucella spp. cgMLST

Issue - State: open - Opened by wjewers 3 months ago - 2 comments
Labels: Status: In Progress

#209 - able to use on assemblies with seq len <100,000 char?

Issue - State: open - Opened by ojessop 4 months ago - 1 comment
Labels: Status: In Progress

#208 - Can I get STs with cgMLST? (cgST)

Issue - State: closed - Opened by juanjo255 6 months ago - 2 comments
Labels: Status: Completed

#207 - keep pyrodigal output in gff

Issue - State: open - Opened by juanjo255 6 months ago - 2 comments
Labels: Type: Enhancement, Type: Question, Status: In Progress

#206 - Feature Request: Add Function to Generate MSA FASTA File Using `results_allele.tsv`

Issue - State: open - Opened by vascokarla 6 months ago - 3 comments
Labels: Type: Enhancement, Status: In Progress

#205 - AlleleCallEvaluator Issue - KeyError

Issue - State: closed - Opened by arshdeep1k 6 months ago - 2 comments
Labels: Status: Completed

#204 - chewbbaca_AlleleCallEvaluator bug

Issue - State: open - Opened by mcanses 7 months ago - 6 comments
Labels: Status: In Progress

#203 - Problem installing chewBBACA on Windows

Issue - State: open - Opened by harayalen 7 months ago - 1 comment

#202 - AlleleCall error : updating hash tables

Issue - State: closed - Opened by LudoPoire 7 months ago - 2 comments

#201 - Typo in tutorial? Wrong version to install with conda

Issue - State: closed - Opened by melparker101 8 months ago - 3 comments
Labels: Status: Completed

#200 - Can I use or add a different translation table for the genetic code (working with parasites)?

Issue - State: closed - Opened by azmigueldario 8 months ago - 7 comments
Labels: Type: Bug, Status: Completed

#199 - AlleleCall - Error in translate_fasta and protein_alignment

Issue - State: closed - Opened by jdaeth274 8 months ago - 3 comments
Labels: Status: Completed

#198 - AlleleCallEvaluator error: cgMLST is composed of 0 loci

Issue - State: closed - Opened by jgugliel 8 months ago - 5 comments
Labels: Type: Bug, Status: Completed

#197 - AlleleCall issue - Error on select_representatives, KeyError

Issue - State: open - Opened by 0mician 11 months ago - 1 comment
Labels: Status: In Progress

#196 - Blast Local IDs too long?

Issue - State: closed - Opened by cizydorczyk 11 months ago - 2 comments
Labels: Status: Completed

#195 - AlleleCall issue - Determining BLASTp self-score for each representative...

Issue - State: open - Opened by daraneda96 12 months ago - 4 comments
Labels: Status: In Progress

#194 - CreateSchema - ValueError: not enough values to unpack (expected 2, got 1)

Issue - State: closed - Opened by daraneda96 12 months ago - 4 comments
Labels: Status: Completed

#193 - Coding strand convention

Issue - State: closed - Opened by a-damC about 1 year ago - 2 comments
Labels: Type: Question, documentation

#192 - Creating conda environment throws error with the latest [3.3.2] version

Issue - State: closed - Opened by anwarMZ about 1 year ago - 2 comments

#192 - Creating conda environment throws error with the latest [3.3.2] version

Issue - State: open - Opened by anwarMZ about 1 year ago - 1 comment
Labels: Status: In Progress

#191 - IndexError

Issue - State: closed - Opened by kayobianco about 1 year ago - 2 comments
Labels: Status: Completed

#190 - print invalid names for simpler warnings which were skipped/missed

Pull Request - State: closed - Opened by chrisgulvik about 1 year ago - 2 comments
Labels: Status: In Progress

#189 - Invalid alleles and invalid genes

Issue - State: closed - Opened by lskatz about 1 year ago - 9 comments
Labels: Status: Completed

#188 - Create git tag for v3.2.0 release

Issue - State: closed - Opened by alanorth over 1 year ago - 2 comments
Labels: Status: Completed

#187 - File not found because of wrong path AlleleCall

Issue - State: closed - Opened by mlarjim over 1 year ago - 3 comments
Labels: Status: Completed

#187 - File not found because of wrong path AlleleCall

Issue - State: closed - Opened by mlarjim over 1 year ago - 3 comments
Labels: Status: Completed

#186 - 3.3.0 AlleleCall reports missing files

Issue - State: closed - Opened by karlkashofer over 1 year ago - 2 comments
Labels: Type: Bug

#186 - 3.3.0 AlleleCall reports missing files

Issue - State: open - Opened by karlkashofer over 1 year ago - 1 comment
Labels: Type: Bug, Status: In Progress

#185 - Newest Pyrodigal breaks chewBBACA

Issue - State: closed - Opened by karlkashofer over 1 year ago - 2 comments
Labels: Type: Bug, Status: Completed

#184 - Documentation issue

Issue - State: open - Opened by karlkashofer over 1 year ago - 3 comments
Labels: Status: In Progress

#184 - Documentation issue

Issue - State: closed - Opened by karlkashofer over 1 year ago - 4 comments
Labels: Status: Completed

#183 - Add Klebsiella pneumoniae ptf

Pull Request - State: closed - Opened by ryanjameskennedy over 1 year ago - 5 comments
Labels: Type: Enhancement, Status: Completed

#183 - Add Klebsiella pneumoniae ptf

Pull Request - State: closed - Opened by ryanjameskennedy over 1 year ago - 5 comments
Labels: Type: Enhancement, Status: Completed

#182 - Ecountering an issue when running AlleleCall

Issue - State: open - Opened by kamivain over 1 year ago - 9 comments
Labels: Status: In Progress

#182 - Ecountering an issue when running AlleleCall

Issue - State: open - Opened by kamivain over 1 year ago - 8 comments
Labels: Status: In Progress

#181 - Chewbbaca visualization output

Issue - State: open - Opened by davidmaimoun over 1 year ago - 1 comment
Labels: Type: Question, Status: In Progress

#181 - Chewbbaca visualization output

Issue - State: open - Opened by davidmaimoun over 1 year ago - 4 comments
Labels: Type: Question, Status: In Progress

#180 - Did the arg `--fr` get dropped?

Issue - State: closed - Opened by russellsmithies over 1 year ago - 3 comments
Labels: Type: Question, Status: Completed

#180 - Did the arg `--fr` get dropped?

Issue - State: closed - Opened by russellsmithies over 1 year ago - 3 comments
Labels: Type: Question, Status: Completed

#179 - Add pyrodigal for gene prediction

Pull Request - State: closed - Opened by rfm-targa over 1 year ago
Labels: Type: Enhancement, Status: Completed

#179 - Add pyrodigal for gene prediction

Pull Request - State: closed - Opened by rfm-targa over 1 year ago
Labels: Type: Enhancement, Status: In Progress

#178 - Add AlleleCallEvaluator module

Pull Request - State: closed - Opened by rfm-targa over 1 year ago
Labels: Type: Enhancement, Status: Completed

#178 - Add AlleleCallEvaluator module

Pull Request - State: closed - Opened by rfm-targa over 1 year ago
Labels: Type: Enhancement, Status: In Progress

#177 - INF not reporting

Issue - State: closed - Opened by jtrew89 over 1 year ago - 3 comments

#177 - INF not reporting

Issue - State: closed - Opened by jtrew89 over 1 year ago - 3 comments

#176 - Issue when using AlleleCall with a large number of genomes

Issue - State: closed - Opened by ccrinconc over 1 year ago - 3 comments

#176 - Issue when using AlleleCall with a large number of genomes

Issue - State: closed - Opened by ccrinconc over 1 year ago - 3 comments

#175 - Adapting external schema for Salmonella enterica from cgmlst.org

Issue - State: closed - Opened by omegatro almost 2 years ago - 2 comments
Labels: Status: Completed

#174 - Improving input file detection.

Pull Request - State: closed - Opened by rfm-targa almost 2 years ago

#174 - Improving input file detection.

Pull Request - State: closed - Opened by rfm-targa almost 2 years ago

#173 - Error: invalid start byte

Issue - State: closed - Opened by eam12 almost 2 years ago - 11 comments
Labels: Status: Completed

#173 - Error: invalid start byte

Issue - State: closed - Opened by eam12 almost 2 years ago - 11 comments
Labels: Status: Completed

#172 - Updates and fixes for SchemaEvaluator

Pull Request - State: closed - Opened by rfm-targa almost 2 years ago
Labels: Type: Enhancement, Status: Completed

#172 - Updates and fixes for SchemaEvaluator

Pull Request - State: closed - Opened by rfm-targa almost 2 years ago
Labels: Type: Enhancement, Status: In Progress

#171 - No possibilty to turn off gene prediction completly

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

#170 - If the input is the eukaryotic group, how can I get the training file?

Issue - State: closed - Opened by alienn233 almost 2 years ago - 1 comment
Labels: Status: Completed

#170 - If the input is the eukaryotic group, how can I get the training file?

Issue - State: closed - Opened by alienn233 almost 2 years ago - 1 comment
Labels: Status: Completed

#169 - Issue with fasta input files

Issue - State: closed - Opened by hkaspersen almost 2 years ago - 3 comments
Labels: Status: Completed

#169 - Issue with fasta input files

Issue - State: closed - Opened by hkaspersen almost 2 years ago - 3 comments
Labels: Status: Completed

#168 - Duplicate alllele id's inserted into the database

Issue - State: closed - Opened by jrober84 almost 2 years ago - 2 comments
Labels: Status: Completed

#168 - Duplicate alllele id's inserted into the database

Issue - State: closed - Opened by jrober84 almost 2 years ago - 2 comments
Labels: Status: Completed

#167 - Get the closest profile

Issue - State: open - Opened by mweberr almost 2 years ago - 1 comment
Labels: Type: Question

#167 - Get the closest profile

Issue - State: open - Opened by mweberr almost 2 years ago - 1 comment
Labels: Type: Question

#166 - Bump webpack from 5.4.0 to 5.76.0 in /CHEWBBACA/SchemaEvaluator/resources/schema_evaluator_main_react_scripts

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#164 - AttributeError: 'NoneType' object has no attribute 'seq'

Issue - State: closed - Opened by famiji almost 2 years ago - 5 comments
Labels: Status: Completed

#164 - AttributeError: 'NoneType' object has no attribute 'seq'

Issue - State: closed - Opened by famiji almost 2 years ago - 5 comments
Labels: Status: Completed

#163 - Error when calling chewBBACA AlleleCall with --cds-input flag

Issue - State: closed - Opened by TorHou almost 2 years ago - 4 comments
Labels: Type: Bug, Priority: High, Status: Completed

#163 - Error when calling chewBBACA AlleleCall with --cds-input flag

Issue - State: closed - Opened by TorHou almost 2 years ago - 4 comments
Labels: Type: Bug, Priority: High, Status: Completed

#162 - how should I handle the column headers when I upload my "results_alleles.tsv" to Phyloviz online

Issue - State: closed - Opened by famiji almost 2 years ago - 1 comment
Labels: Type: Question, Status: Completed

#161 - How can I obtain the file "excluded_genomes.txt"? And how was the file "GBS_assembly_stats.tsv" generated? Thank you for your response.

Issue - State: closed - Opened by yolo2fh almost 2 years ago - 2 comments
Labels: Type: Question, Status: Completed

#160 - Errno 2 FileNotFoundError : both for CreateSchema and AlleleCall

Issue - State: closed - Opened by ainus1022 almost 2 years ago - 4 comments
Labels: Status: Completed

#160 - Errno 2 FileNotFoundError : both for CreateSchema and AlleleCall

Issue - State: closed - Opened by ainus1022 almost 2 years ago - 4 comments
Labels: Status: Completed

#159 - SchemaEvaluator: html output files for individual gene cannot be displayed in browser

Issue - State: closed - Opened by artmisk13 almost 2 years ago - 9 comments
Labels: Type: Bug, Status: Completed

#159 - SchemaEvaluator: html output files for individual gene cannot be displayed in browser

Issue - State: closed - Opened by artmisk13 almost 2 years ago - 9 comments
Labels: Type: Bug, Status: In Progress

#156 - Bugfix for missing BLASTp raw scores

Pull Request - State: closed - Opened by rfm-targa about 2 years ago
Labels: Type: Bug, Type: Enhancement, Priority: High, Status: Completed

#156 - Bugfix for missing BLASTp raw scores

Pull Request - State: closed - Opened by rfm-targa about 2 years ago
Labels: Type: Bug, Type: Enhancement, Priority: High, Status: Completed

#155 - Can we specify file names of input assemblies?

Issue - State: open - Opened by MostafaYA about 2 years ago - 1 comment

#155 - Can we specify file names of input assemblies?

Issue - State: open - Opened by MostafaYA about 2 years ago - 1 comment

#154 - AlleleCall error due to a specific gene

Issue - State: closed - Opened by MostafaYA about 2 years ago - 8 comments
Labels: Type: Bug, Priority: High, Status: Completed

#153 - Update ExtractCgMLST module

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

#153 - Update ExtractCgMLST module

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

#149 - Bump minimatch and serve in /CHEWBBACA/SchemaEvaluator/resources/schema_evaluator_main_react_scripts

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 2 comments
Labels: dependencies

#149 - Bump minimatch and serve in /CHEWBBACA/SchemaEvaluator/resources/schema_evaluator_main_react_scripts

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 2 comments
Labels: dependencies

#148 - Bump minimatch and serve in /CHEWBBACA/SchemaEvaluator/resources/schema_evaluator_individual_reports_react_scripts

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 2 comments
Labels: dependencies

#148 - Bump minimatch and serve in /CHEWBBACA/SchemaEvaluator/resources/schema_evaluator_individual_reports_react_scripts

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 2 comments
Labels: dependencies

#147 - AlleleCall - optimization for small datasets

Pull Request - State: closed - Opened by rfm-targa over 2 years ago
Labels: Type: Enhancement, Status: Completed

#146 - Allele calling threshold

Issue - State: closed - Opened by mlarjim over 2 years ago - 5 comments
Labels: Type: Question, documentation, Status: Completed