Ecosyste.ms: Issues

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GitHub / davidemms/OrthoFinder issues and pull requests

#819 - How Accurate are Species-Specific Orthogroups?

Issue - State: open - Opened by Cronzo almost 2 years ago - 2 comments

#817 - Primary transcripts

Issue - State: closed - Opened by maggs-x almost 2 years ago - 7 comments

#816 - orthofinder part of somethings went wrongs

Issue - State: open - Opened by yuwanziaaa almost 2 years ago - 1 comment

#815 - no progress on a very large collection of proteins

Issue - State: open - Opened by rocpengliu almost 2 years ago

#814 - Species Tree seems incorrect

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

#813 - Error in match_fasta2gff... Orthofinder can't handle this

Issue - State: closed - Opened by nirwan1265 almost 2 years ago - 1 comment

#812 - inconsistent newick format

Issue - State: open - Opened by nhartwic almost 2 years ago - 9 comments

#811 - Node Support for Species Tree With Paralogous Orthogroups

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

#810 - Running IQTREE or RAxML separately

Issue - State: open - Opened by m3hdad almost 2 years ago - 2 comments

#809 - OSError: [Errno 23] Too many open files in system

Issue - State: closed - Opened by TANGLi83-star almost 2 years ago - 1 comment

#808 - Single copy genes

Issue - State: closed - Opened by LI-zijian1 almost 2 years ago - 2 comments

#807 - expected memory usage

Issue - State: open - Opened by nhartwic almost 2 years ago

#806 - Error running Orthofinder prior to generating trees

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

#805 - diamond --max-target-seqs 0

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

#804 - How to annotate orthogroups?

Issue - State: open - Opened by Ruiqi-CUB almost 2 years ago

#803 - Orthofinder not finishing with large genome

Issue - State: closed - Opened by morenon3 almost 2 years ago - 1 comment

#802 - Just building the tree with OrthoFinder

Issue - State: open - Opened by Ruiqi-CUB almost 2 years ago

#801 - Error while gene tree and species tree estimation

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

#800 - Hidden files with the extension of .faa

Issue - State: open - Opened by goshng almost 2 years ago

#799 - Orthofinder giving really unexpected results

Issue - State: open - Opened by kkrizanovic almost 2 years ago - 1 comment

#798 - obstacles in using script in 2.5.4

Issue - State: open - Opened by lilvyan almost 2 years ago

#797 - Which output file is best?

Issue - State: open - Opened by SheepwormJM almost 2 years ago - 1 comment

#796 - lack of supporting values in SpeciesTree_rooted.txt

Issue - State: open - Opened by Mirror1211 almost 2 years ago

#795 - Orthofinder stuck for long after running MCL

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

#793 - orthofinder installation error on mac

Issue - State: open - Opened by SAMANDOLL almost 2 years ago - 2 comments

#792 - Running OrthoFInder, getting error code 137:

Issue - State: open - Opened by mmotoc almost 2 years ago - 1 comment

#791 - Bus Error

Issue - State: open - Opened by nhartwic almost 2 years ago

#790 - Alignment must have at least 3 sequences in test iqtree

Issue - State: open - Opened by WJT0925 almost 2 years ago

#789 - Test can run "iqtree" - failed

Issue - State: closed - Opened by WJT0925 almost 2 years ago - 4 comments

#786 - Add LAST search option

Pull Request - State: open - Opened by kullrich almost 2 years ago

#784 - Zero Single copy genes from Orthofinder analysis

Issue - State: open - Opened by nitinra almost 2 years ago - 4 comments

#781 - OrthologousGroups.txt does not exist

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

#780 - Orthofinder fails at Gene Distances for large dataset

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

#779 - MSA failure (no known reason)

Issue - State: open - Opened by drabe004 almost 2 years ago - 7 comments

#778 - orthofinder computation time on very big data

Issue - State: open - Opened by alambard about 2 years ago - 2 comments

#777 - Several problems

Issue - State: open - Opened by abhijeetsingh1704 about 2 years ago - 1 comment

#776 - Analysis for Orthofinder

Issue - State: open - Opened by Calvin2077 about 2 years ago

#775 - Python 3.11 depreciation

Issue - State: closed - Opened by SwiftSeal about 2 years ago - 1 comment

#774 - Identifying and Extracting paralogs

Issue - State: open - Opened by naahraissa about 2 years ago

#773 - How to analyse Orthofinder results

Issue - State: open - Opened by mictadlo about 2 years ago

#771 - Number of orthogroups containing species

Issue - State: open - Opened by lopires about 2 years ago

#770 - identify genes in groups

Issue - State: open - Opened by mictadlo about 2 years ago

#769 - cannot run test data

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

#768 - Version 2.5.4 NewickError Unexisting tree file but I can find tree file

Issue - State: open - Opened by OliviaAgatha about 2 years ago - 7 comments

#767 - Compared with synteny analysis

Issue - State: open - Opened by gouwei1 about 2 years ago

#766 - OrthoFinder - Part 2 is not deterministic

Issue - State: open - Opened by raufs about 2 years ago - 2 comments

#764 - ERROR: Cannot run diamond

Issue - State: open - Opened by Oelsakha about 2 years ago - 2 comments

#763 - TypeError: expected string or bytes-like object

Issue - State: closed - Opened by Oelsakha about 2 years ago - 1 comment

#762 - The same gene in multiple orthogroups

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

#761 - primary_transcript.py does not return one isoform per gene

Issue - State: open - Opened by tsackton about 2 years ago - 3 comments

#760 - ValueError: invalid mode: 'rU'

Issue - State: closed - Opened by alexzaccaron about 2 years ago - 3 comments

#758 - Finding how many clusters and genes organisms have

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

#756 - Query about N0.tsv output

Issue - State: open - Opened by SheepwormJM about 2 years ago

#755 - Statistical analysis of clustered gene families

Issue - State: open - Opened by mictadlo about 2 years ago

#753 - Install issue on M1 Macbook Pro via conda

Issue - State: closed - Opened by clementfkent about 2 years ago - 1 comment

#751 - Number of species-specific orthogroups

Issue - State: closed - Opened by zhangwenda0518 about 2 years ago

#750 - Running Orthofinder for multiple species

Issue - State: open - Opened by azizebrahimi over 2 years ago - 1 comment

#749 - Malformatted line in Blast0_0.txt & ERROR: Blast0_0.txt is corrupted

Issue - State: closed - Opened by yuan102379 over 2 years ago - 2 comments

#746 - Optimize analysis speed, update diamond (V2.07)

Issue - State: open - Opened by sunjiahe-hub over 2 years ago - 3 comments

#741 - Orthofinder, MSA has failed

Issue - State: open - Opened by stephen-14 over 2 years ago - 1 comment

#740 - Unassigned Genes VS OGs which include only one gene

Issue - State: open - Opened by Tdanis over 2 years ago - 3 comments

#738 - Orthofinder does not run further than blast

Issue - State: open - Opened by Estherrr1997 over 2 years ago - 3 comments

#735 - Malformatted line in Blast#_#.txt

Issue - State: open - Opened by mch246 over 2 years ago - 4 comments

#725 - FastTree failed

Issue - State: open - Opened by CongLiu37 over 2 years ago - 1 comment

#723 - ModuleNotFoundError: No module named 'scipy'

Issue - State: open - Opened by TommySalvetti01 over 2 years ago - 3 comments

#710 - Test can run "raxml" - failed

Issue - State: open - Opened by peter-hu-up over 2 years ago - 4 comments

#706 - UnicodeDecodeError

Issue - State: open - Opened by khoojj over 2 years ago - 6 comments

#705 - Orthofinder Analysis on 128 proteomes stuck

Issue - State: open - Opened by DamianRio over 2 years ago - 2 comments

#694 - Bus error w/ large run

Issue - State: open - Opened by dborgesr over 2 years ago - 1 comment

#686 - ERROR: Cannot run diamond

Issue - State: closed - Opened by gouwei1 almost 3 years ago - 7 comments

#684 - ERROR: Cannot run mmseqs | but I can use mmseqs

Issue - State: open - Opened by wuyudelan almost 3 years ago - 6 comments

#663 - OrthoFinder generates BLAST files with NUL characters and is unhappy

Issue - State: closed - Opened by ltsypin almost 3 years ago - 7 comments

#644 - Orthofinder error

Issue - State: open - Opened by nicholasprice79 about 3 years ago - 2 comments

#637 - Diamond makedb failed error in tutorial

Issue - State: open - Opened by ld9866 over 3 years ago - 3 comments

#619 - ERROR: Cannot run user-configured tree method 'iqtree'

Issue - State: closed - Opened by fciamponi over 3 years ago - 4 comments

#614 - create_files_for_hogs :: not installed by setpu.py

Issue - State: open - Opened by EricDeveaud over 3 years ago - 3 comments

#608 - OrthologuesStats_many-to-one and OrthologuesStats_one-to-many?

Issue - State: closed - Opened by goshng over 3 years ago - 1 comment

#603 - diamond makedb error

Issue - State: open - Opened by wthomas14 over 3 years ago - 1 comment

#571 - Reducing Open Files

Issue - State: open - Opened by niederhuth over 3 years ago - 9 comments

#566 - STRIDE ERROR

Issue - State: open - Opened by lisiruiyu over 3 years ago - 4 comments

#564 - ValueError: too many values to unpack

Issue - State: open - Opened by etcProfile over 3 years ago - 15 comments

#559 - Best way to choose one orthologous sequences per species per Orthologous group

Issue - State: open - Opened by LucieGL over 3 years ago - 11 comments

#526 - WARNING: Unexpected error local variable 'iog' referenced before assignment

Issue - State: closed - Opened by camille-puginier almost 4 years ago - 16 comments