Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / chklovski/CheckM2 issues and pull requests

#125 - Update python version support

Issue - State: open - Opened by ialarmedalien about 1 month ago

#124 - Reliable completeness scores for endosymbiont genomes?

Issue - State: open - Opened by gavinmdouglas about 1 month ago

#122 - Descriptions of the columns in the output file

Issue - State: open - Opened by harper357 3 months ago

#119 - Models not loading for test run

Issue - State: open - Opened by spennino1 4 months ago

#117 - dependency issue

Issue - State: open - Opened by EJS01 4 months ago

#115 - Bug on a fresh install

Issue - State: open - Opened by asaldivar93 5 months ago - 2 comments

#114 - Runing Checkm2 using MiDAS db

Issue - State: open - Opened by Hedi65 5 months ago

#112 - UnicodeEncodeError when running testrun and on real data.

Issue - State: open - Opened by patriciatran 6 months ago - 2 comments

#111 - AF_UNIX path too long

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

#110 - TypeError: split() error

Issue - State: open - Opened by marshjw 7 months ago - 6 comments

#109 - Naming Output TSV File

Issue - State: open - Opened by emilyhyde 8 months ago - 1 comment

#108 - Check for errors from calling DIAMOND

Pull Request - State: open - Opened by luispedro 8 months ago

#107 - Database download failed

Issue - State: open - Opened by jtamames 9 months ago - 3 comments

#106 - test run yields different results

Issue - State: closed - Opened by jorondo1 9 months ago - 1 comment

#105 - Testrun ERROR: No DIAMOND annotation was generated.

Issue - State: open - Opened by Mayurk619 9 months ago - 4 comments

#102 - Can Checkm2 be fine-tuned for euMAGs?

Issue - State: closed - Opened by Andyargueasae 10 months ago - 1 comment

#101 - coding density

Issue - State: open - Opened by lianzhh 11 months ago

#100 - TypeError: metaclass conflict

Issue - State: open - Opened by laczik-git 11 months ago - 9 comments

#99 - Database update?

Issue - State: open - Opened by cmkobel 11 months ago - 2 comments

#98 - Random errors on clusters

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

#95 - Error in DIAMOND execution

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

#94 - the version checkm2 v1.0.2 was not available on conda

Issue - State: closed - Opened by quliping about 1 year ago - 1 comment

#92 - Question about Checkm2 Annotation

Issue - State: open - Opened by aljazdzy about 1 year ago - 1 comment

#91 - Cannot install ChekM2

Issue - State: closed - Opened by jehaab about 1 year ago - 1 comment

#90 - How to remove the contamination sequence from MAGs

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

#89 - Average_Gene_Length

Issue - State: closed - Opened by Sumsarium about 1 year ago - 1 comment

#88 - [Question] How to determine the number of splits used for Diamond annotation?

Issue - State: open - Opened by jolespin about 1 year ago - 1 comment

#87 - Can I use protein fasta as input?

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

#86 - Updated README with CheckM2 testrun numbers

Pull Request - State: open - Opened by pommevilla over 1 year ago - 1 comment

#85 - checkm2 database --download fail

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

#84 - N50 values

Issue - State: open - Opened by mallen6 over 1 year ago

#83 - KeyError: 'key' while downloading database

Issue - State: open - Opened by yazhinia over 1 year ago - 6 comments

#82 - running checkm2 issue

Issue - State: open - Opened by chantellyu over 1 year ago - 8 comments

#81 - Small test diamond db

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

#80 - checkmsum issue

Issue - State: open - Opened by francesco-ricci over 1 year ago - 2 comments

#79 - running checkm2 on a large number of genomes

Issue - State: open - Opened by sherlyn99 over 1 year ago - 2 comments

#77 - test run giving higher completeness than expected

Issue - State: closed - Opened by sherlyn99 over 1 year ago - 1 comment

#76 - When test running, it says, Error, DIAMOND failed to generate output

Issue - State: open - Opened by Abelcanc3rhack3r over 1 year ago - 8 comments

#75 - OSError: [Errno 16] Device or resource busy: '.nfs00000000000a4c9d00005011'

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

#74 - Cannot download Diamond db

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

#73 - OSError: [Errno 30] Read-only file system

Issue - State: open - Opened by cmkobel over 1 year ago - 3 comments

#72 - There was a problem installing the database

Issue - State: closed - Opened by ylei14 over 1 year ago - 5 comments

#71 - Include more stats

Issue - State: closed - Opened by Sumsarium over 1 year ago - 1 comment

#70 - Incompatible packages when installing through conda/mamba

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

#69 - can't install checkm2

Issue - State: open - Opened by francesco-ricci over 1 year ago - 4 comments

#68 - added Dockerfile to get CheckM2 in docker and singularity

Pull Request - State: open - Opened by Louis-MG over 1 year ago

#67 - Big Data Analysis

Issue - State: closed - Opened by RoyaRahmani over 1 year ago - 1 comment

#66 - unexpected end of input in testrun

Issue - State: closed - Opened by JingqiuLiao over 1 year ago - 1 comment

#65 - Saved models could not be loaded: 'str' object has no attribute 'decode'

Issue - State: open - Opened by xinehc over 1 year ago - 7 comments

#64 - Unexpected result when running checkm2 testrun

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

#63 - Package would be ignored: data models testrun version

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

#62 - Checkm2 dev

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

#61 - Include `mamba` option for installation instructions

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

#60 - Related to locale

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

#58 - No catching diamond job failures?

Issue - State: open - Opened by nick-youngblut almost 2 years ago - 8 comments

#56 - what the version of the gtdb taxonomy database, release xxx?

Issue - State: closed - Opened by Caiyulu-818 almost 2 years ago

#55 - UnicodeEncodeError

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

#54 - Testrun discrepancies

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

#53 - OSError: [Errno 95] Operation not supported

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

#52 - failure to reproduce Completeness data from Supplementary Table 6

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

#51 - Visualization

Issue - State: closed - Opened by namnh7 almost 2 years ago - 1 comment

#50 - database downloading fails

Issue - State: closed - Opened by ye00ye almost 2 years ago - 3 comments

#49 - Unable to install scikit-learn==0.23.2

Issue - State: open - Opened by sjaenick almost 2 years ago - 1 comment
Labels: enhancement

#48 - specify dependecy versions

Issue - State: closed - Opened by nick-youngblut about 2 years ago - 7 comments

#47 - Version of Numpy installed from conda

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

#46 - [Discussion] Testing on microeukaryotic organisms as a negative control

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

#45 - [Dependency Request] Generalize the dependency versions

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

#44 - CheckM2 dev

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

#43 - CheckM2 dev

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

#42 - I cannot run CheckM2 in Diamond

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

#41 - quality report: *.gz extension removed from file name

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

#40 - checkm2 predict: diamond annotations as input

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

#39 - PermissionError: diamond_path.json

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

#38 - grpcio dependency: No such file or directory: 'cc'

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

#37 - Checkm 2 fails when a genome has lowercase bases

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

#36 - Some questions about NCBI archaeal genomes predicted as Low-quality draft

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

#35 - Runs out of /tmp space. Needs option to specify temp dir

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

#34 - Increase protein search stringency? (Low-homology problem)

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

#33 - --allmodels is broken.

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

#32 - CheckM2 too conservative?

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

#31 - Database invalid version

Issue - State: closed - Opened by lmrodriguezr about 2 years ago - 7 comments

#30 - Update installation to 1.0.0

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

#29 - (Bio)conda

Issue - State: closed - Opened by lfenske-93 about 2 years ago - 1 comment

#28 - UnicodeEncodeError

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

#27 - Assessing the quality of viral bins

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

#26 - insufficient for CUDA runtime version?

Issue - State: closed - Opened by raw937 over 2 years ago - 1 comment

#25 - Latest software and database versions

Issue - State: closed - Opened by donovan-h-parks over 2 years ago - 2 comments
Labels: documentation