Ecosyste.ms: Issues

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

GitHub / kblin/ncbi-genome-download issues and pull requests

#232 - file type requested not found in NCBI

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

#231 - Using ncbi-genome-download package

Issue - State: closed - Opened by ChillarAnand 4 months ago - 4 comments

#229 - Download genomes from assembly file

Issue - State: closed - Opened by ChillarAnand 4 months ago - 1 comment

#228 - Recent issue downloading from GenBank but not RefSeq

Issue - State: closed - Opened by raufs 5 months ago - 1 comment
Labels: not a bug

#227 - Update issue templates

Pull Request - State: closed - Opened by kblin 5 months ago

#226 - issue with ncbi-genome-download

Issue - State: closed - Opened by SrichandanPadhi 5 months ago - 1 comment
Labels: not a bug

#225 - KeyError: 'assembly_accession'

Issue - State: closed - Opened by biotemon 5 months ago - 1 comment

#224 - Failing during checking assembly?

Issue - State: open - Opened by Thomieh73 6 months ago - 1 comment
Labels: question

#223 - Host Link Could be Incorrect

Issue - State: open - Opened by Mohammed-Quraishi 9 months ago - 2 comments
Labels: not shipped yet

#222 - ncbi-genome-download shows error "Unsupported group"

Issue - State: closed - Opened by Anju-h 9 months ago - 4 comments

#220 - can it download genomes of specific strains?

Issue - State: closed - Opened by Liao-PRIC 12 months ago - 1 comment
Labels: question

#219 - No downloads matched error

Issue - State: closed - Opened by tasha99 about 1 year ago - 2 comments
Labels: question

#216 - /path error when running ncbi-genome-download in a shell script

Issue - State: open - Opened by KinSimon96 about 1 year ago - 1 comment
Labels: need info

#215 - gimme_taxa.py / ngd mismatched format

Issue - State: open - Opened by zreitz about 1 year ago - 2 comments
Labels: not shipped yet

#214 - Collect author info from other ncbi-genome-download contributors.

Issue - State: open - Opened by kblin over 1 year ago
Labels: enhancement

#211 - Update summary.py

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

#210 - Allow for fuzzy match of assembly summary header

Pull Request - State: closed - Opened by chasemc over 1 year ago - 9 comments

#209 - KeyError: 'assembly_accession'

Issue - State: closed - Opened by scorreard over 1 year ago - 17 comments

#208 - Support for filtering assemblies by sequencing platform?

Issue - State: closed - Opened by JonathanAbrahams1337 over 1 year ago - 3 comments

#207 - How can I reference ncbi-genome-download

Issue - State: closed - Opened by padpadpadpad over 1 year ago - 11 comments

#206 - Can't download unclassified organisms

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

#205 - Number of genomes downloaded not corresponding to number of entries

Issue - State: open - Opened by arfaiq over 1 year ago - 1 comment

#203 - Check if accessions has CDS?

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

#202 - Option for metadata file only

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

#201 - Update config.py

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

#200 - Download hangs with no output when given long .txt file

Issue - State: closed - Opened by Tylersuard almost 2 years ago

#199 - Feature request: filter by length of sequence

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

#197 - Databases version

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

#196 - Missing genomes when downloading with genura

Issue - State: open - Opened by WEIGUO93 about 2 years ago

#194 - Error while downloading genera

Issue - State: open - Opened by sanyalab over 2 years ago

#193 - Downloading of cDNA, GFF3, and EST sequences

Issue - State: open - Opened by sanyalab over 2 years ago

#191 - Download problem

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

#180 - Can the software specify the output file name

Issue - State: closed - Opened by Achuan-2 over 2 years ago
Labels: question

#179 - perfect match option?

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

#178 - All virus download errors

Issue - State: closed - Opened by xiaozhangzhang123 over 2 years ago - 1 comment

#177 - Enhancements based on official API

Issue - State: closed - Opened by 444thLiao almost 3 years ago - 1 comment

#176 - Add ngd to biocontainers?

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

#175 - doanload failed when groups is set to all

Issue - State: closed - Opened by showteeth about 3 years ago - 5 comments
Labels: not shipped yet

#174 - ERROR: No downloads matched your filter. Please check your options.

Issue - State: open - Opened by jolespin about 3 years ago - 1 comment

#144 - Connection Error, RemoteDisconnected

Issue - State: closed - Opened by lisavader over 3 years ago - 18 comments

#143 - Pseudogenes download

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

#142 - Filenames with genus, species and strain?

Issue - State: open - Opened by johanneswerner almost 4 years ago

#141 - Reference sequence

Issue - State: open - Opened by kate-simonova almost 4 years ago

#140 - problems downloading genome

Issue - State: open - Opened by Timmywang1 almost 4 years ago - 1 comment

#139 - Some RefSeq genomes not being downloaded

Issue - State: open - Opened by sskashaf about 4 years ago

#138 - Not downloading suppressed or replaced Refseq assembly accessions

Issue - State: open - Opened by BobFukkink about 4 years ago - 5 comments

#137 - Error using annotate

Issue - State: closed - Opened by IsabelFE about 4 years ago - 3 comments
Labels: not a bug

#136 - .faa.gz files not being downloaded for bacteria

Issue - State: open - Opened by BhushanDhamale about 4 years ago - 8 comments
Labels: bug

#135 - gimme_taxa.py: sqlite3.IntegrityError

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

#134 - Feature request: Download a number of accession IDs ...

Issue - State: closed - Opened by phiweger about 4 years ago - 3 comments
Labels: question

#133 - Document valid -R or --refseq-categories REFSEQ_CATEGORIES values

Issue - State: closed - Opened by peterjc about 4 years ago - 7 comments
Labels: not shipped yet

#132 - Fixed typo in command line API help

Pull Request - State: closed - Opened by peterjc about 4 years ago - 1 comment

#131 - This app is not responding....

Issue - State: closed - Opened by furqan915 about 4 years ago - 2 comments

#130 - Checking if RefSeq genome available or not without downloading?

Issue - State: open - Opened by nahid18 about 4 years ago - 2 comments
Labels: enhancement, help wanted

#129 - No downloads matched your filter

Issue - State: closed - Opened by nahid18 about 4 years ago - 4 comments
Labels: question

#127 - Minor updates to gimme_taxa.py

Pull Request - State: closed - Opened by jrjhealey over 4 years ago

#126 - Metadata and download

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

#125 - Add progress bar #28

Pull Request - State: closed - Opened by 444thLiao over 4 years ago

#124 - Issue download protozoa genomes

Issue - State: closed - Opened by mw55309 over 4 years ago - 8 comments
Labels: duplicate

#122 - Removing zombie processes

Pull Request - State: closed - Opened by Wrzlprmft over 4 years ago - 1 comment

#121 - Any idea how to load this into database, ideally PostgreSQL?

Issue - State: closed - Opened by MironAtHome over 4 years ago - 2 comments
Labels: question

#120 - High memory consumption (50 GB) for genbank bacteria

Issue - State: open - Opened by openpaul over 4 years ago - 9 comments
Labels: enhancement, help wanted

#119 - Download genomes based on accession number

Issue - State: closed - Opened by donovan-h-parks over 4 years ago - 3 comments
Labels: question

#118 - Issue downloading archaea genomes in RefSeq

Issue - State: closed - Opened by Puumanamana over 4 years ago - 5 comments

#117 - raise warning if refseq metagenome is requested

Pull Request - State: closed - Opened by openpaul over 4 years ago - 1 comment

#116 - NCBI-genome-download not working with no errors

Issue - State: open - Opened by sepidehalamouti over 4 years ago - 6 comments

#115 - Metagenomes is not a valid group in refseq

Issue - State: open - Opened by openpaul over 4 years ago
Labels: not shipped yet

#114 - Check if the ftp directory listed is NA when filtering

Pull Request - State: closed - Opened by openpaul over 4 years ago

#113 - Na fix

Pull Request - State: closed - Opened by openpaul over 4 years ago - 1 comment

#112 - fix and update translation of Chinese version

Pull Request - State: closed - Opened by llxlr over 4 years ago - 1 comment

#111 - made gimme_taxa.py an installable script

Pull Request - State: closed - Opened by ialbert over 4 years ago - 1 comment

#110 - anyway to exclude plasmid sequences from genomes downloaded?

Issue - State: open - Opened by Liao-PRIC over 4 years ago - 1 comment

#109 - no option for translated CDS format

Issue - State: open - Opened by mattmelnicki almost 5 years ago - 2 comments

#108 - Connection issue due to ftp address?

Issue - State: closed - Opened by elzerac almost 5 years ago - 2 comments

#107 - Downloading a Genbank accession ("GCA_*")

Issue - State: closed - Opened by jayrbolton almost 5 years ago - 1 comment

#106 - Fill metadata table after the download jobs are created

Pull Request - State: closed - Opened by axbazin almost 5 years ago - 1 comment

#105 - metadata option unworking

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

#104 - Error Connection

Issue - State: closed - Opened by Nilad almost 5 years ago - 2 comments
Labels: not a bug

#103 - Checking MD5SUM in parallel when more than one process is allowed

Pull Request - State: closed - Opened by axbazin almost 5 years ago - 1 comment

#102 - incomplete descended taxid output of gimme_taxa.py

Issue - State: closed - Opened by 444thLiao about 5 years ago - 2 comments

#101 - How to cite this package?

Issue - State: open - Opened by vinisalazar about 5 years ago - 3 comments

#100 - Question about mitochondrial genomes

Issue - State: closed - Opened by ucbtmae about 5 years ago - 2 comments
Labels: question

#99 - problems downloading representative genome

Issue - State: open - Opened by jotech about 5 years ago - 4 comments

#97 - translate README.md into Chinese

Pull Request - State: closed - Opened by llxlr about 5 years ago - 2 comments

#96 - ngd as a module: quiet mode

Issue - State: closed - Opened by asetGem about 5 years ago - 5 comments
Labels: enhancement, not shipped yet

#95 - Download from NCBI failed: ConnectionError

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

#94 - translate README.md into Chinese

Pull Request - State: closed - Opened by llxlr over 5 years ago

#93 - i want to translate README.md

Issue - State: closed - Opened by llxlr over 5 years ago - 4 comments
Labels: enhancement, not shipped yet

#92 - Is it possible to download all genomes belonging to species of a viral genus ?

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

#91 - download for different groups

Issue - State: closed - Opened by semihorhanbio over 5 years ago - 3 comments
Labels: question, not shipped yet

#90 - download for different groups

Issue - State: closed - Opened by semihorhanbio over 5 years ago

#89 - core: remove print statement for type material

Pull Request - State: closed - Opened by Cptmorgan27 over 5 years ago - 1 comment

#88 - download of all archaeal sequences from genbank fails

Issue - State: closed - Opened by johanneswerner over 5 years ago - 7 comments
Labels: bug

#87 - Handle IndexError when value for organism_name is abnormal

Pull Request - State: closed - Opened by andrewsanchez over 5 years ago - 4 comments