motu-tool/mOTUs issues and pull requests

#126 - fix typos and add some code to motus db installation

Pull Request - State: open - Opened by lilithfeer about 2 months ago

#125 - Error: Cannot call bwa on the file ERR4563329.fastq.gz

Issue - State: open - Opened by xiangjianmao 4 months ago - 2 comments

#124 - PIP releases miss the motus.remove.padded.sh file

Issue - State: open - Opened by d-goryslavets 4 months ago - 1 comment
Labels: bug

#123 - GTDB Taxonomy for Version 3.1.0

Issue - State: closed - Opened by G-Molano-LA 4 months ago - 1 comment

#122 - profile output looks wired

Issue - State: open - Opened by lrt666 4 months ago - 1 comment

#121 - Request for Support: Galaxy Integration of mOTUs Tool

Issue - State: open - Opened by Alby-Git 7 months ago - 8 comments

#120 - Update GTDB taxonomy

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

#119 - what about the overview of the content of the all species involved in the database？

Issue - State: closed - Opened by fanqiedantang 7 months ago - 1 comment

#118 - mOTUs 3 and corresponding taxonomy of GTDB

Issue - State: closed - Opened by huminfo8 8 months ago - 1 comment

#117 - Count table output?

Issue - State: closed - Opened by ayabrown 9 months ago - 2 comments

#116 - Update to use GTDB 214

Issue - State: closed - Opened by Ge0rges 10 months ago - 1 comment

#115 - Incompatible with new versions of samtools?

Issue - State: closed - Opened by Ge0rges 10 months ago - 1 comment

#114 - Compatibility between 2.5 and 3.0 mOTUs.

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

#113 - ImportError: No module named motus.motus

Issue - State: closed - Opened by snehamurthy21 about 1 year ago - 2 comments
Labels: question

#112 - Strange inconsistant row in mOTUs output

Issue - State: closed - Opened by xapple about 1 year ago - 3 comments
Labels: question

#111 - Motus 3.1.0

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

#110 - zipped input files

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

#109 - Expose path to download database for `downloadDB` as a user input

Issue - State: open - Opened by valentynbez over 1 year ago - 6 comments
Labels: enhancement, question, next version

#108 - Genome size normalization

Issue - State: closed - Opened by ramanujamr over 1 year ago - 3 comments
Labels: question

#107 - missing motus.remove.padded.sh file in conda for v3.0.3

Issue - State: closed - Opened by psecekartal over 1 year ago - 6 comments
Labels: help wanted

#106 - no abundance

Issue - State: closed - Opened by ucassee over 1 year ago - 3 comments
Labels: help wanted

#105 - Inconsistencies in the mOTUs3 - genome metadata

Issue - State: closed - Opened by fplaza over 1 year ago - 3 comments
Labels: bug

#104 - is mOTUs suitable for Metatranscriptome sequence?

Issue - State: closed - Opened by zhaoxvwahaha over 1 year ago - 1 comment
Labels: help wanted

#103 - Consistency for `taxonomy` and `full-taxonomy` output

Issue - State: open - Opened by valentynbez over 1 year ago - 2 comments
Labels: enhancement, next version

#102 - Improve header consistency for better machine parsing

Issue - State: open - Opened by valentynbez over 1 year ago
Labels: enhancement, next version

#101 - [DOCS] citation

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

#100 - Possible to cache DB?

Issue - State: closed - Opened by wwood over 1 year ago - 2 comments
Labels: help wanted

#99 - Fix wrong computation of read length

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

#98 - Incomplete species annotation in the GTDB file?

Issue - State: closed - Opened by cotillau over 1 year ago - 2 comments
Labels: bug

#97 - missing GTDB classification for motus_3 ids

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

#96 - I want to know where the database is downloaded and installed.

Issue - State: closed - Opened by luozhy88 almost 2 years ago - 2 comments
Labels: question

#95 - GTDB mOTUs taxonomy ?

Issue - State: closed - Opened by tapj almost 2 years ago - 3 comments
Labels: enhancement

#94 - Long reads

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

#93 - list of taxa present in the mOTUs database?

Issue - State: closed - Opened by rjsorr about 2 years ago - 1 comment
Labels: question

#92 - help to create a small database for testing

Issue - State: closed - Opened by jianhong about 2 years ago - 8 comments
Labels: help wanted

#91 - Error extending mOTU 2.5.1 database

Issue - State: closed - Opened by Xentrics about 2 years ago - 6 comments
Labels: help wanted

#90 - mOTUs

Issue - State: closed - Opened by Jibowe over 2 years ago - 3 comments
Labels: question

#89 - no unassigned with full taxonomy

Issue - State: closed - Opened by gitcat01 over 2 years ago - 1 comment
Labels: question

#88 - Pypi package `motus` is something else, instructions outdated

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

#87 - conda install motus stuck in Executing transaction

Issue - State: closed - Opened by dengzq1234 over 2 years ago - 21 comments
Labels: help wanted

#86 - Motus302

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

#85 - Clarify ref-mOTUs taxonomic annotation

Issue - State: closed - Opened by AlessioMilanese over 2 years ago - 3 comments
Labels: question

#84 - Database Extension

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

#83 - Possible error in help for 'motus map_tax'

Issue - State: closed - Opened by mikemc over 2 years ago - 3 comments
Labels: enhancement

#82 - Map file for v3 database

Issue - State: closed - Opened by trickovicmatija over 2 years ago - 2 comments
Labels: help wanted

#81 - Know how much of an environment is covered

Issue - State: closed - Opened by SilasK over 2 years ago - 9 comments
Labels: question

#80 - Output mode with individual read assignments?

Issue - State: closed - Opened by sjaenick over 2 years ago - 3 comments
Labels: enhancement

#79 - motus calc_motu: -p ignored if -A given

Issue - State: closed - Opened by sjaenick over 2 years ago - 1 comment
Labels: enhancement

#78 - Conda motus-3.0.1

Issue - State: closed - Opened by plmeta almost 3 years ago - 7 comments
Labels: help wanted

#77 - Error with append.py

Issue - State: closed - Opened by Alexey-Kovtun almost 3 years ago - 6 comments
Labels: question

#76 - Improve ref-mOTUs taxonomy annotation at level higher than species

Issue - State: closed - Opened by AlessioMilanese almost 3 years ago - 1 comment
Labels: enhancement

#75 - question about isolate sequencing data

Issue - State: closed - Opened by franciscozorrilla almost 3 years ago - 3 comments
Labels: question

#74 - problem installing mOTU

Issue - State: closed - Opened by Jigyasa3 almost 3 years ago - 3 comments
Labels: help wanted

#73 - Improve interface

Pull Request - State: closed - Opened by AlessioMilanese about 3 years ago - 1 comment

#72 - Improve the ref-mOTUs taxonomy

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

#71 - Ileibacterium appears twice in mOTU v2.6.1

Issue - State: closed - Opened by metaganal about 3 years ago - 2 comments
Labels: bug

#70 - Version2.6.1

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

#69 - Phylogenetic tree for mOTUs version 2.6.0

Issue - State: open - Opened by haegih about 3 years ago - 11 comments
Labels: enhancement, next version

#68 - Updated test that setup.py was run

Pull Request - State: closed - Opened by matthpich about 3 years ago - 1 comment

#67 - snv_call changes

Issue - State: closed - Opened by hjruscheweyh about 3 years ago

#66 - [Feature request] conda installation without the dbs

Issue - State: closed - Opened by matthpich about 3 years ago - 2 comments
Labels: question

#65 - OTU clustering/distance matrix of marker-genes from different samples

Issue - State: closed - Opened by Jigyasa3 about 3 years ago - 1 comment
Labels: question

#64 - misplaced sys.exit

Issue - State: closed - Opened by hjruscheweyh over 3 years ago - 1 comment
Labels: bug

#63 - Availability of MAGs representative of meta-mOTUs

Issue - State: closed - Opened by fplaza over 3 years ago - 5 comments
Labels: question

#62 - Version2.6

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

#61 - The genus `Ileibacterium` appears twice in the output (genus mode)

Issue - State: closed - Opened by luispedro over 3 years ago - 4 comments
Labels: bug

#60 - How to match subset fastq to motus?

Issue - State: closed - Opened by zckoo007 over 3 years ago - 3 comments
Labels: help wanted

#59 - metaSNV results is empty

Issue - State: closed - Opened by taylorreiter almost 4 years ago - 2 comments
Labels: help wanted

#58 - Only zeros in abundance result

Issue - State: closed - Opened by pavelmedina almost 4 years ago - 3 comments
Labels: help wanted

#57 - Large fq file, low read counts

Issue - State: closed - Opened by mgosborn almost 4 years ago - 14 comments
Labels: help wanted

#56 - Can I compare the fasta files to motus database?

Issue - State: closed - Opened by zckoo007 almost 4 years ago - 2 comments
Labels: question

#55 - Getting [mpileup] and [E::hts_open_format] errors when running motus snv_call

Issue - State: closed - Opened by CLGLynnsane almost 4 years ago - 5 comments
Labels: bug

#54 - which CDS is meta_12476?

Issue - State: closed - Opened by zckoo007 almost 4 years ago - 4 comments
Labels: question

#53 - Identification down to strain level

Issue - State: closed - Opened by termithorbor almost 4 years ago - 1 comment
Labels: question

#52 - motus profile can't output the bam file [Issue with samtools 1.10]

Issue - State: closed - Opened by Shinexy99 about 4 years ago - 8 comments
Labels: bug

#51 - Normalizing metagenomic gene relative abundance using MOTU2

Issue - State: closed - Opened by Jigyasa3 about 4 years ago - 4 comments
Labels: question

#50 - [E::main] Try to download again the motus profiler

Issue - State: closed - Opened by max1c about 4 years ago - 23 comments

#49 - issue with old versions of `samtools`

Issue - State: closed - Opened by AlessioMilanese over 4 years ago
Labels: wontfix

#48 - show read fate - headers from fastq

Issue - State: open - Opened by handibles over 4 years ago - 17 comments
Labels: enhancement, next version

#47 - Own Database

Issue - State: closed - Opened by EllenOldenburg over 4 years ago - 6 comments
Labels: help wanted

#46 - Can not download db_mOTU_v2.5.1.tar.gz

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

#45 - Taxonomic annotation of mOTUs in v2.5

Issue - State: closed - Opened by theavanrossum over 4 years ago - 10 comments
Labels: enhancement

#44 - Problem when adding my own genomes to the reference db

Issue - State: closed - Opened by lsayaved over 4 years ago - 5 comments
Labels: bug

#43 - Problem with the Map_snv wiki page

Issue - State: closed - Opened by mikemc over 4 years ago - 1 comment

#42 - Recommended usage with paired-end reads

Issue - State: closed - Opened by mikemc over 4 years ago - 7 comments
Labels: help wanted

#41 - tax level clarification

Issue - State: closed - Opened by jzrapp over 4 years ago - 4 comments
Labels: question

#40 - help with installation - SSL: CERTIFICATE_VERIFY_FAILED

Issue - State: closed - Opened by jzrapp over 4 years ago - 2 comments
Labels: help wanted

#39 - Possible to obtain percent nucleotide divergence from `motus svn_call` output?

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

#38 - Classify Nanopore reads?

Issue - State: closed - Opened by angelovangel over 4 years ago - 1 comment
Labels: question

#37 - Quick question regarding identification of eukaryotes

Issue - State: closed - Opened by Anto007 over 4 years ago - 3 comments
Labels: question

#36 - What does mean the last row of output ?

Issue - State: closed - Opened by ryo-aoki3 almost 5 years ago - 1 comment
Labels: question

#35 - Phylogeny of the mOTUs?

Issue - State: closed - Opened by mikemc almost 5 years ago - 5 comments
Labels: question

#34 - updates for 2.5.1

Pull Request - State: closed - Opened by AlessioMilanese almost 5 years ago

#33 - Is it possible to use fasta files instead of fastq files and get the number of marker genes assigned to it?

Issue - State: closed - Opened by Jigyasa3 almost 5 years ago - 5 comments
Labels: question

#32 - Error with CAMI result

Issue - State: closed - Opened by AlessioMilanese almost 5 years ago - 1 comment
Labels: bug

#31 - M ot us2.5

Pull Request - State: closed - Opened by AlessioMilanese almost 5 years ago

#30 - Surprising results - No unmapped reads

Issue - State: closed - Opened by sturne29 almost 5 years ago - 2 comments
Labels: help wanted

#29 - Very few reads can be mapped

Issue - State: closed - Opened by yaohuayang-uva almost 5 years ago - 8 comments
Labels: help wanted

#28 - Mouse metagenomic DB

Issue - State: closed - Opened by kunstner about 5 years ago - 6 comments
Labels: enhancement, question

#27 - Support for Pavian

Issue - State: closed - Opened by Anto007 about 5 years ago - 9 comments
Labels: enhancement

GitHub / motu-tool/mOTUs issues and pull requests