Ecosyste.ms: Issues

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

GitHub / shandley/hecatomb issues and pull requests

#118 - "Invalid database read" Error: creattsv died

Issue - State: open - Opened by RyCrobe 2 months ago - 1 comment

#117 - Process secondary_nt_calc_lca failed

Issue - State: open - Opened by pengouy 5 months ago - 1 comment

#116 - Hecatomb test error

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

#115 - Another error in processing mmseqs_contig_annotation

Issue - State: open - Opened by pengouy 5 months ago - 1 comment

#114 - Failed job in processing secondary_nt_calc_lca step

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

#113 - Long reads support

Issue - State: open - Opened by owenkuo-TW 5 months ago - 5 comments

#112 - ERROR: Snakemake failed

Issue - State: open - Opened by baidefeng 6 months ago - 4 comments

#111 - Adding an ID blacklist file

Pull Request - State: open - Opened by linsalrob 6 months ago - 1 comment
Labels: enhancement

#110 - Hecatomb not working ( secondary aa taxonomy)

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

#109 - bugfixes

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

#108 - hecatomb.config.yaml

Issue - State: closed - Opened by wuhuiyun07 9 months ago - 1 comment

#107 - hecatomb combine not working

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

#106 - Placeholder of length limit

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

#105 - Dev

Pull Request - State: closed - Opened by beardymcjohnface 10 months ago

#104 - Errors in newest version 1.3.0

Issue - State: open - Opened by pengouy 10 months ago - 15 comments

#103 - Dev

Pull Request - State: closed - Opened by beardymcjohnface 10 months ago

#102 - unit test updates

Pull Request - State: closed - Opened by beardymcjohnface 10 months ago

#101 - ModuleNotFoundError: No module named 'attrmap'

Issue - State: closed - Opened by Eddylusamaki 11 months ago - 1 comment

#100 - 98, 99% Failure Issue

Issue - State: open - Opened by Key-man-fromArchive 11 months ago - 1 comment

#99 - out-of-memory error during population_assembly.flye, STAGE: repeat

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

#98 - add-host is failing on mask_host

Issue - State: open - Opened by beardymcjohnface about 1 year ago - 3 comments

#97 - No rule to produce assembly

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

#96 - Filtering out host (human) genome beforehand?

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

#95 - bigtable.tsv column question

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

#94 - Dev

Pull Request - State: closed - Opened by beardymcjohnface over 1 year ago

#93 - Update dev

Pull Request - State: closed - Opened by beardymcjohnface over 1 year ago

#92 - Dev

Pull Request - State: closed - Opened by beardymcjohnface over 1 year ago

#89 - Dev

Pull Request - State: closed - Opened by beardymcjohnface over 1 year ago

#88 - Skip host removal

Issue - State: closed - Opened by beardymcjohnface over 1 year ago - 1 comment
Labels: enhancement

#87 - HPC Execution problem when changing to V.1.1.0

Issue - State: closed - Opened by luisalbertoc95 almost 2 years ago - 4 comments

#86 - HPC database installation problems

Issue - State: closed - Opened by lucyintheskyzzz almost 2 years ago - 31 comments

#85 - I want to create a web app for hecatomb.

Issue - State: open - Opened by Key-man-fromArchive almost 2 years ago - 1 comment

#84 - Enhancement: add whitelist to pre-processing

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

#83 - assembly Contigs in results folder

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

#82 - readthedocs viral ecology R tutorial error fix

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

#81 - Dev

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

#80 - Check for the presence of an environment variable for location of databases

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

#79 - Illumina_NextSeq_Run dies immediately

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

#78 - flye crash in population_assembly step

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

#77 - mmseqs: command not found

Issue - State: closed - Opened by alanorth over 2 years ago - 7 comments

#76 - fastp not building

Issue - State: closed - Opened by beardymcjohnface over 2 years ago - 8 comments

#75 - Missing new line in contigAnnotations.tsv

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

#74 - crash unknown

Issue - State: closed - Opened by Vikash84 over 2 years ago - 1 comment

#73 - bring new updates into dev

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

#72 - Merge pull request #70 from SarahBeecroft/main

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

#71 - Add in round A/B seq functionality

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

#70 - Adding single end and fastp functions

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

#69 - Error in rule SECONDARY_AA_refactor_finalize

Issue - State: closed - Opened by Leran10 over 2 years ago - 1 comment

#68 - missing fields in outfile

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

#67 - taxonomy improvement

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

#66 - Enhancement: Host

Issue - State: open - Opened by mihinduk almost 3 years ago - 5 comments
Labels: enhancement

#65 - MANY missing output files; Input files updated by another job

Issue - State: closed - Opened by mihinduk almost 3 years ago - 1 comment

#64 - Database installation problems

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

#63 - Mmseqs update

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

#62 - Dev

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

#61 - Error in secondary_nt_lca_table step

Issue - State: closed - Opened by Leran10 almost 3 years ago - 11 comments

#60 - Error executing PRIMARY_NT_reformat

Issue - State: closed - Opened by shandley almost 3 years ago - 1 comment

#59 - Java Runtime Error when running test databases on VM

Issue - State: closed - Opened by blusoldier001 almost 3 years ago - 43 comments

#58 - Documentation

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

#57 - Partition phage and eukaryotic viruses

Issue - State: open - Opened by shandley almost 3 years ago - 1 comment
Labels: enhancement

#56 - snakemake profiles

Issue - State: closed - Opened by linsalrob almost 3 years ago - 2 comments
Labels: bug

#54 - Dev

Pull Request - State: closed - Opened by henr0089 almost 3 years ago

#52 - hecatomb install giving error

Issue - State: closed - Opened by Vikash84 almost 3 years ago - 5 comments

#51 - Dev

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

#50 - new version number

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

#49 - Dev

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

#48 - Example Profile Broken

Issue - State: closed - Opened by gbouras13 almost 3 years ago - 2 comments

#47 - Run Offline

Issue - State: closed - Opened by gbouras13 almost 3 years ago - 2 comments

#46 - Problem with running

Issue - State: closed - Opened by wertick01 about 3 years ago - 11 comments

#45 - does --configfile work with the download script?

Issue - State: closed - Opened by beardymcjohnface about 3 years ago - 1 comment

#44 - settings in '--configfile' file not passed to 'script:' rules

Issue - State: closed - Opened by beardymcjohnface about 3 years ago - 1 comment

#43 - Hecatomb v1.0.0.beta.2 crash

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

#42 - Dev

Pull Request - State: closed - Opened by beardymcjohnface about 3 years ago

#41 - Dev

Pull Request - State: closed - Opened by beardymcjohnface about 3 years ago

#40 - updating hecatomb

Issue - State: closed - Opened by mihinduk about 3 years ago - 1 comment

#39 - kill switch

Issue - State: closed - Opened by mihinduk about 3 years ago - 1 comment

#38 - mouse

Issue - State: closed - Opened by mihinduk about 3 years ago - 1 comment

#37 - Error in rule PRIMARY_NT_reformat

Issue - State: closed - Opened by Leran10 about 3 years ago - 4 comments

#36 - pipeline requires higher version of conda which has --conda-frontend parameter

Issue - State: closed - Opened by Leran10 about 3 years ago - 3 comments

#35 - hecatomb's same output files from the same dataset are with different sizes

Issue - State: closed - Opened by Leran10 about 3 years ago - 10 comments

#34 - missing python package

Issue - State: closed - Opened by mihinduk about 3 years ago - 1 comment

#33 - Dev

Pull Request - State: closed - Opened by beardymcjohnface about 3 years ago

#32 - Dev

Pull Request - State: closed - Opened by beardymcjohnface about 3 years ago

#31 - Dev

Pull Request - State: closed - Opened by beardymcjohnface over 3 years ago

#30 - Contaminant removal update

Pull Request - State: closed - Opened by beardymcjohnface over 3 years ago

#29 - megahit -> flye reformatting

Issue - State: closed - Opened by mihinduk almost 4 years ago - 1 comment

#28 - For NextSeq samples, maximum HTCF memory insufficient for merge seqtable step in R

Issue - State: closed - Opened by mihinduk almost 4 years ago - 1 comment

#27 - flye "Looks like the system ran out of memory"

Issue - State: closed - Opened by mihinduk about 4 years ago - 3 comments

#23 - Update phage lineages

Issue - State: closed - Opened by linsalrob about 4 years ago

#22 - Streamline file zipping and unzipping

Issue - State: closed - Opened by shandley about 4 years ago

#21 - Streamline fastq vs fasta file usage

Issue - State: closed - Opened by shandley about 4 years ago

#20 - additional script to merge new data with old at seqtable_merge.R level

Issue - State: closed - Opened by mihinduk about 4 years ago - 3 comments
Labels: enhancement

#19 - convert_phyloseq.R

Issue - State: closed - Opened by linsalrob about 4 years ago - 1 comment