Ecosyste.ms: Issues

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

GitHub / biobakery/MetaPhlAn issues and pull requests

#229 - FIX: metaphlan4 bowtie2-build --threads flag bug

Pull Request - State: open - Opened by heloint 6 months ago

#226 - Fix typo

Pull Request - State: open - Opened by bernt-matthias 6 months ago

#225 - Add helpful error messages to read_fastx.py

Pull Request - State: closed - Opened by Pandapip1 9 months ago - 3 comments

#224 - [BUG]:Mamba installation - transaction Error

Issue - State: closed - Opened by WUD2018 11 months ago - 1 comment

#223 - failed to download Chocophlan Database

Issue - State: closed - Opened by rishidash12 11 months ago - 1 comment

#222 - [BUG]Could not locate a Bowtie index corresponding to basename

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

#221 - Actinomyces Viscosus

Issue - State: closed - Opened by lear-711 about 1 year ago - 1 comment

#218 - Merge_metaphlan_table.py Error

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

#217 - Correspondence between SGBs and specific strain names

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

#216 - Revamp issue creation options

Pull Request - State: closed - Opened by Pandapip1 over 1 year ago - 7 comments

#215 - NOT getting to run it

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

#214 - [BUG] mpa_vJan21_CHOCOPhlAnSGB_202103 cannot used

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

#212 - reduce update frequency during download

Pull Request - State: open - Opened by kdm9 over 1 year ago

#211 - FileNotFoundError: [Errno 2] Metaphlan4_Data_SGB2GTDB.tsv

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

#210 - [BUG] MetaPhlAn ignores database.

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

#209 - Help with customising the database

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

#208 - empty output

Issue - State: closed - Opened by javad30 almost 2 years ago - 1 comment

#207 - #Question

Issue - State: closed - Opened by JiaZhong28 almost 2 years ago - 1 comment

#206 - Fix typo in merge_metaphlan_tables.py

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

#205 - nreads of bowtie2 file

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

#204 - A strange result

Issue - State: closed - Opened by TKsh6 almost 2 years ago - 1 comment

#202 - bowtie2-align exited with value 137

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

#201 - How to get mpa_vOct22_CHOCOPhlAnSGB_202212.nwk for calculate_diversity.r?

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

#200 - UnicodeDecodeError

Issue - State: closed - Opened by TKsh6 almost 2 years ago - 1 comment

#199 - Solving environment failed

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

#198 - [BUG]

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

#197 - [BUG] MetaPhlAn 4.0.4 h5py/numpy version issue

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

#196 - [BUG] bowtie database not found

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

#195 - I keep getting "MD5 checksums do not correspond!...." error

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

#194 - -t rel_ab_w_read_stats output error

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

#193 - Sample2markers speedup

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

#192 - Unable to use --install[BUG]

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

#190 - No MetaPhlAn BowTie2 database found

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

#189 - [BUG] mpa_vJan21_CHOCOPhlAnSGB_202103_species.txt.bz2 is not complete

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

#188 - [BUG] Metaphlan wiki typo

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

#187 - [BUG]

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

#186 - How to Install metaphlan4?

Issue - State: closed - Opened by yhg926 over 2 years ago - 1 comment

#185 - List of taxa in Metaphlan4 database

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

#183 - [BUG] metaphlan 4 beta KeyError: 't'

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

#182 - Dropbox files no longer exist: cannot install database

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

#181 - MetaPhlAn3: IndexError: list index out of range

Issue - State: closed - Opened by y1025i over 2 years ago - 1 comment

#180 - Integration of vsc code in new MP-repo

Pull Request - State: closed - Opened by azufre451 over 2 years ago

#179 - [BUG]cannot find hclust2.py

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

#178 - Update metaphlan2krona.py

Pull Request - State: closed - Opened by sarah872 over 2 years ago

#177 - metaphlan2krona.py

Issue - State: closed - Opened by sarah872 over 2 years ago - 2 comments

#176 - classify to superkingdom/kingdom level?

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

#175 - Metaphlan3 classification - comparison of samples and RiboDetector

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

#174 - Unable to download from Dropbox [BUG]

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

#173 - [BUG] - merge_metaphlan_tables.py not working in 3.0.14

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

#172 - Use tempfile for marker file for extract_markers.py

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

#171 - Check for a partial bowtie2 database build

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

#170 - running metaphlan on rnaseq data

Issue - State: closed - Opened by marco91sol about 3 years ago - 1 comment

#169 - Tranformation of the abundance table into relative abundance.

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

#168 - customize database

Issue - State: closed - Opened by wjj666 about 3 years ago

#166 - Metaphlan2 could annotated 100% bacteria but metaphlan3 annotated 100% UNKNOWN

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

#165 - strainphlan

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

#163 - metaphlan2krona.py not working

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

#162 - Problems about species absence and new information about database update

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

#161 - L. casei & B. subtilis group not present in MetaPhlAn 3

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

#160 - Database already present error

Issue - State: closed - Opened by cirodri1 over 3 years ago - 7 comments

#159 - strainphlan: directory does not exist

Issue - State: closed - Opened by nick-youngblut over 3 years ago

#158 - --force_download

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

#157 - metaphlan -install --bowtie2db $path[BUG]

Issue - State: closed - Opened by XiongGZ over 3 years ago

#155 - v3.0.12 alpha, unknown estimate changes

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

#154 - Merge bug list error

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

#152 - [BUG] conda MetaPhlAn3 tries to write into conda install tree

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

#151 - [BUG]

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

#150 - Attempt to Change File Permissions Causes Software Abort

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

#149 - metaphlan fails with division by 0 error

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

#148 - Installing database error

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

#147 - Contradictory Positional Arguments Specification

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

#146 - [BUG]utils/merge_metaphlan_tables.py

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

#145 - Database and bowtie issues

Issue - State: closed - Opened by WebBach almost 4 years ago - 5 comments

#144 - add COVID-19 to database

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

#143 - run all clades once

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

#142 - Add install of database folder in setup because if database folder is…

Pull Request - State: closed - Opened by ljmciver almost 4 years ago - 4 comments

#141 - Add missing type of analysis in documentation

Pull Request - State: closed - Opened by bebatut almost 4 years ago

#140 - UNKNOWN too high

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

#138 - [BUG] rel_ab_w_read_stats with --add_viruses throws KeyError: 'PRJNA14242'

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

#137 - Issue for database file full_chocophlan.v296_201901.tar.gz

Issue - State: closed - Opened by deminu about 4 years ago - 6 comments

#136 - Release version 3.0

Pull Request - State: closed - Opened by fbeghini about 4 years ago

#135 - ZeroDivisionError: float division by zero

Issue - State: closed - Opened by Caelyn996 about 4 years ago - 11 comments

#134 - ZeroDivisionError: float division by zero

Issue - State: closed - Opened by Caelyn996 about 4 years ago - 1 comment

#133 - Question About StrainPhlAn3 Polymorphic Output File

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

#132 - [BUG] MetaPhlan3 produces no bowtie2out

Issue - State: closed - Opened by iquasere about 4 years ago - 6 comments

#131 - Metaphlan 3 issue reading gzipped paired end input

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

#130 - Running with paired-end data generates bowtie file but not txt file

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