bierinformatik / mirnature Goto Github PK
View Code? Open in Web Editor NEWBona fide miRNA annotation tool
License: GNU General Public License v3.0
Bona fide miRNA annotation tool
License: GNU General Public License v3.0
When use makeblastdb to create fasta indexes, appears this warning:
Possible precedence issue with control flow operator at /home/user/anaconda3/envs/mirnature/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
Seems that it was reported as a corrected bug for Bioperl 1.7.8:
bioperl/bioperl-live@6459750
Hello!
I got following error with miRNAture:
miRNAture -stage complete -dataF ~/public_db/miRNAture/Dataset_mirnature_Sept21_2022/Data -speG ~/public_db/model_insects/Drosophila_melanogaster_GCF_000001215.4.fna -speN Drosophila_mirna -speT mrna -w ~/pipeline_eval/miRNAture/Drosophila -m blast,hmm,rfam,mirbase,infernal,final -pe 0 -str 5,6 -blstq ~/public_db/miRBase -debug_mode 1
Attribute (nbitscore_cut) does not pass the type constraint because: Validation failed for 'Num' with value at constructor Mir::ConfigurationFile::new (defined at /home/c/c-liu/miniconda3/envs/mirnature/lib/perl5/site_perl/Mir/ConfigurationFile.pm line 631) line 192
Mir::ConfigurationFile::new('Mir::ConfigurationFile', 'stage', 'complete', 'species_name', 'Drosophila_mirna', 'species_tag', 'mrna', 'species_genome', '~/public_db/model_insects/Drosophila_melanogaster_GCF_000001215.4.fna', 'output_folder', '~/pipeline_eval/miRNAture/Drosophila', 'data_path', '~/public_db/miRNAture/Dataset_mirnature_Sept21_2022/Data', 'current_folder', '/home/c/c-liu/Hpc/pipeline_eval', 'model_list', undef, 'mirfix_path', '', 'mode', 'blast,hmm,rfam,mirbase,infernal,final', 'repetition_rules', '', 'nbitscore_cut', '', 'blast_strategy', 'ARRAY(0x55dd789bd5f0)', 'blast_queries_path', '~/public_db/miRBase', 'user_folder', '', 'parallel_linux', 0, 'parallel', 0, 'debug_mode', 1, 'evaluation_results_folder', '~/pipeline_eval/miRNAture/Drosophila/Final_miRNA_evaluation', 'mirnanchor_folder', '~/pipeline_eval/miRNAture/Drosophila/miRNA_validation') called at /home/c/c-liu/miniconda3/envs/mirnature/bin/miRNAture line 101
How to fix it?
SIncerely,
Cong
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.