Ecosyste.ms: Issues

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GitHub / BigDataBiology/SemiBin issues and pull requests

#188 - Does 'torch.load' have effect on the result?

Issue - State: open - Opened by guangingmai 4 days ago - 2 comments

#187 - [QUESTION] Which options are deprecated in SemiBin2?

Issue - State: open - Opened by rdenise 9 days ago - 1 comment

#184 - Improve/added schema to epimetheus output

Pull Request - State: closed - Opened by SebastianDall 20 days ago

#183 - Finished without creating output_bins

Issue - State: open - Opened by Sung-hub about 1 month ago - 1 comment

#181 - Handling Fungal Genomes in Mixed Metagenomic Datasets

Issue - State: open - Opened by PlantHealth-Analytics about 2 months ago - 1 comment

#179 - Multi-sample binning using fairy coverage

Issue - State: open - Opened by Louis-MG 3 months ago - 1 comment

#176 - DAS Tool

Issue - State: closed - Opened by francesco-ricci 5 months ago - 2 comments

#175 - Warnings when binning using long reads.

Issue - State: open - Opened by 123chenshixin 5 months ago

#174 - KeyError(f"None of [{key}] are in the [{axis_name}]") using aemb

Issue - State: open - Opened by michoug 6 months ago - 3 comments

#173 - Number of bins prior to reclustering: 0

Issue - State: open - Opened by yazhinia 6 months ago - 1 comment

#172 - Error: provided pretrained model only used in single-sample binning!

Issue - State: open - Opened by yazhinia 6 months ago - 3 comments

#170 - Error: Running hmmsearch fail

Issue - State: open - Opened by StickHu 7 months ago - 2 comments

#169 - How to run "generate_sequence_features_single" with UNSORTED bam

Issue - State: open - Opened by GuoYang-qd 7 months ago - 2 comments

#168 - KeyError when generating coverage

Issue - State: closed - Opened by Louis-MG 7 months ago - 3 comments

#166 - SemiBin2 fails to generate bins for large assemblies

Issue - State: closed - Opened by apcamargo 8 months ago - 3 comments

#164 - Training step problem

Issue - State: open - Opened by heavennew 9 months ago - 2 comments

#163 - Only 2 contigs contain 1000 basepairs

Issue - State: closed - Opened by timternetnet 10 months ago - 3 comments

#162 - Extract then merge

Pull Request - State: open - Opened by alienzj 10 months ago - 9 comments

#161 - bam files from bowtie2 or strobealign

Issue - State: closed - Opened by microsud 11 months ago - 2 comments

#160 - removed

Issue - State: closed - Opened by eperezv 11 months ago

#159 - Error when running SemiBin2 (normalization?)

Issue - State: open - Opened by eperezv 12 months ago - 6 comments

#158 - Accept CRAM files instead of BAM

Issue - State: closed - Opened by fplaza 12 months ago - 3 comments

#156 - special character in sample names

Issue - State: closed - Opened by gjordaopiedade 12 months ago - 1 comment

#155 - Too many open files

Issue - State: closed - Opened by susheelbhanu 12 months ago - 11 comments

#154 - Empty data.csv file and IndexError with SemiBin2

Issue - State: closed - Opened by AAwan2 12 months ago - 6 comments

#153 - Changing default compression from none to gzip will cause DAS tool to fail

Issue - State: closed - Opened by ElderMedic almost 1 year ago - 3 comments

#151 - KeyError: '40075' Easy coassembly binning mode

Issue - State: open - Opened by gabrieleghiotto about 1 year ago - 2 comments

#150 - SemiBin doesnt complete bining. Seems to be stuck

Issue - State: open - Opened by HitMonk about 1 year ago - 4 comments

#149 - Multi-binning got KeyError

Issue - State: closed - Opened by chenjh356 about 1 year ago - 6 comments

#148 - Add option to bypass coverage calculation

Issue - State: closed - Opened by fplaza about 1 year ago - 9 comments

#147 - Empty test cases

Issue - State: open - Opened by Ralwoss over 1 year ago

#146 - Clarification on concatenate_fasta Dereplication Process

Issue - State: closed - Opened by vsanchez0 over 1 year ago - 2 comments

#145 - Replicability of semibin2 single_easy_bin

Issue - State: closed - Opened by FelipeMSD over 1 year ago - 2 comments

#144 - Multi-sample approach and bowtie2-build

Issue - State: closed - Opened by FelipeMSD over 1 year ago - 11 comments

#143 - Error: SemiBin concatenate_fasta

Issue - State: closed - Opened by FelipeMSD over 1 year ago - 4 comments

#142 - Parallel binning

Issue - State: closed - Opened by FelipeMSD over 1 year ago - 2 comments

#141 - Database Download & Documentation

Issue - State: open - Opened by gbouras13 over 1 year ago - 5 comments

#140 - Semibin not respecting `-p` threads argument

Issue - State: open - Opened by AroneyS over 1 year ago - 1 comment

#138 - Long_read problem

Issue - State: open - Opened by ZarulHanifah over 1 year ago - 1 comment

#137 - SemiBin crashes when the last batch has only one element

Issue - State: closed - Opened by fplaza over 1 year ago - 2 comments

#136 - Specifiy the numpy version

Issue - State: closed - Opened by shenwei356 over 1 year ago - 5 comments

#135 - Cannot run on CAMI Skin / VAMB

Issue - State: closed - Opened by richardlett almost 2 years ago - 3 comments

#134 - Bug fix samtools error when testing

Pull Request - State: closed - Opened by psj1997 almost 2 years ago

#133 - KeyError

Issue - State: closed - Opened by Sumsarium almost 2 years ago - 6 comments

#132 - abundance analysis of bin

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

#131 - Running `bedtools genomecov` failed

Issue - State: closed - Opened by nashanghenzan almost 2 years ago - 3 comments

#130 - Failing to index concatenated fasta

Issue - State: closed - Opened by x-rv almost 2 years ago - 1 comment

#129 - Error running single_easy_bin on coassembly

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

#128 - Error using multi_easy_bin with --no-recluster

Issue - State: closed - Opened by Ralwoss about 2 years ago - 8 comments

#127 - GPU utilization

Issue - State: closed - Opened by strejcem about 2 years ago - 8 comments

#126 - SemiBin2 released?

Issue - State: closed - Opened by rdenise about 2 years ago - 4 comments

#125 - ENH Fix FutureWarning in Pandas

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

#124 - Feature request: implement "circular aware" binning

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

#123 - Feature request: TSV with mapping contigs -> bins

Issue - State: closed - Opened by luispedro about 2 years ago - 4 comments

#122 - Update long read binning

Pull Request - State: closed - Opened by psj1997 about 2 years ago

#121 - mtrand.pyx

Issue - State: closed - Opened by hildebra over 2 years ago - 15 comments

#120 - ENH training with self-supervised learning

Pull Request - State: closed - Opened by psj1997 over 2 years ago

#119 - prefix naming

Issue - State: closed - Opened by bartns over 2 years ago - 2 comments

#118 - How to install SemiBin on a server without network

Issue - State: closed - Opened by huizhen-yan over 2 years ago - 1 comment

#117 - document Advanced workflows section

Issue - State: closed - Opened by zpinocchio over 2 years ago - 1 comment

#116 - GTDB config error

Issue - State: closed - Opened by zpinocchio over 2 years ago - 2 comments

#115 - Better output

Pull Request - State: closed - Opened by luispedro over 2 years ago

#114 - Fix typo in docs

Pull Request - State: closed - Opened by sjaenick over 2 years ago - 1 comment

#113 - Feature request: Supply gene prediction via external file

Issue - State: closed - Opened by sjaenick over 2 years ago - 2 comments

#112 - Bug fix atomicwrite on NFS

Pull Request - State: closed - Opened by psj1997 over 2 years ago

#110 - OSError: Failure in running bedtools AND BrokenPipeError: [Errno 32] Broken pipe

Issue - State: closed - Opened by PeterCx over 2 years ago - 2 comments

#109 - eukaryotic genomes

Issue - State: closed - Opened by Thexiyang over 2 years ago - 2 comments

#108 - invalid ELF header

Issue - State: closed - Opened by palomo11 over 2 years ago - 4 comments

#106 - OSError: [Errno 12] Cannot allocate memory

Issue - State: closed - Opened by joeyclancy over 2 years ago - 10 comments

#105 - About GPU-mode

Issue - State: closed - Opened by joeyclancy over 2 years ago - 4 comments

#104 - CRAM support

Issue - State: closed - Opened by hildebra over 2 years ago - 1 comment

#103 - Error during coverage calculation

Issue - State: closed - Opened by rhysnewell over 2 years ago - 5 comments

#102 - Small reference database or test taxonomy TSV file

Issue - State: closed - Opened by bebatut over 2 years ago - 25 comments

#101 - Error: can't open input file /tmp/tmpkm_<x>/contig_<x>.fa. with version 1.01

Issue - State: closed - Opened by ohickl over 2 years ago - 3 comments

#100 - The issue of GTDB reference database

Issue - State: closed - Opened by zh8008 over 2 years ago - 5 comments

#98 - SemiBin has been running for 3 days without any process updates

Issue - State: closed - Opened by lexinwei over 2 years ago - 3 comments

#97 - single_easy_bin failing [Errno 22] Invalid argument

Issue - State: closed - Opened by jserrana almost 3 years ago - 4 comments

#96 - errors running single_easy_bin

Issue - State: closed - Opened by Luponsky almost 3 years ago - 5 comments

#95 - Pretrained models and multiple BAM files

Issue - State: closed - Opened by rhysnewell almost 3 years ago - 4 comments

#94 - SemiBin resources and runtime when ran over CAMI2 data

Issue - State: closed - Opened by Paupiera almost 3 years ago - 8 comments

#92 - single_easy_bin failing with pytorch error

Issue - State: closed - Opened by jamesabbott almost 3 years ago - 4 comments

#91 - RuntimeError: mat1 and mat2 shapes cannot be multiplied

Issue - State: closed - Opened by ckeuschn almost 3 years ago - 7 comments
Labels: bad-error-message

#90 - Error: MD5 check failed, removing '/home/people/binson/.cache/SemiBin/mmseqs2-GTDB/GTDB_v95.tar.gz'.

Issue - State: closed - Opened by B-1991-ing almost 3 years ago - 6 comments
Labels: bad-error-message

#89 - Failed hmmsearch call still produces (wrong, empty) output

Issue - State: closed - Opened by luispedro almost 3 years ago

#88 - Minor improvements

Pull Request - State: closed - Opened by luispedro almost 3 years ago