Ecosyste.ms: Issues

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GitHub / ncbi/datasets issues and pull requests

#350 - Release updated docs for 16.12.1

Pull Request - State: closed - Opened by BradHolmes 9 months ago

#349 - Release updated docs for 16.12.0

Pull Request - State: closed - Opened by BradHolmes 9 months ago

#348 - Accessing annotation from nuccore sequences

Issue - State: closed - Opened by manulera 9 months ago - 1 comment
Labels: enhancement

#347 - Many REST API examples fail on the documentation page

Issue - State: open - Opened by ialbert 9 months ago - 1 comment

#345 - Unable to locate the source code

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

#344 - Error in download

Issue - State: closed - Opened by edtankian97 10 months ago - 2 comments
Labels: bug

#343 - Release updated docs for 16.10.2

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

#342 - GenBank or RefSeq

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

#341 - invalid or unsupported assembly accession: NC_001740

Issue - State: closed - Opened by ggl2151 10 months ago - 1 comment
Labels: question

#340 - Limited number of genome downloads for some taxon

Issue - State: closed - Opened by mkdevesh 10 months ago - 4 comments

#339 - Release updated docs for 16.10.1

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

#338 - Include more metadata from genbank files in virus reports, e.g. `/note` and `/strain`

Issue - State: closed - Opened by corneliusroemer 10 months ago - 2 comments
Labels: enhancement

#337 - Make more publication metadata available via `datasets download virus genome taxon 186538`

Issue - State: closed - Opened by corneliusroemer 10 months ago - 2 comments
Labels: enhancement

#335 - Release updated docs for 16.10.0

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

#334 - request for changelog - do not understand release notes

Issue - State: closed - Opened by conchoecia 10 months ago - 1 comment
Labels: enhancement

#333 - Release updated docs for 16.9.0

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

#332 - Create issue templates

Pull Request - State: closed - Opened by BradHolmes 10 months ago - 1 comment

#330 - Release updated docs for 16.8.1

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

#329 - datasets Version 16.7?

Issue - State: closed - Opened by balags1 11 months ago - 2 comments
Labels: bug

#328 - `ncbi_dataset/data/data_report.jsonl` sometimes missing

Issue - State: closed - Opened by bernt-matthias 11 months ago - 2 comments
Labels: bug

#327 - Feature Request: bgzip option

Issue - State: closed - Opened by genignored 11 months ago - 1 comment
Labels: enhancement

#326 - --geo-location flag runs into invalid zip archive error

Issue - State: open - Opened by joverlee521 11 months ago - 3 comments
Labels: bug

#325 - "Large multi-isolate projects" field in `datasets summary genome` / `dataformat tsv` ?

Issue - State: closed - Opened by paulimer 11 months ago - 2 comments
Labels: enhancement

#324 - Versioning and backwards compatibility

Issue - State: closed - Opened by muffato 11 months ago - 2 comments

#323 - Order of output datasets

Issue - State: closed - Opened by alvanuffelen 11 months ago - 1 comment
Labels: enhancement

#322 - Release updated docs for 16.6.0

Pull Request - State: closed - Opened by BradHolmes 11 months ago

#321 - 404 on annotation_report when assembly has no annotations

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

#320 - Extra info in summary output

Issue - State: closed - Opened by fgvieira 11 months ago - 5 comments

#319 - Questions on ZIP packages and JSON files

Issue - State: closed - Opened by fgvieira 11 months ago - 1 comment
Labels: enhancement

#318 - exit code 1 - rehydration error

Issue - State: closed - Opened by lytt18 11 months ago - 5 comments
Labels: enhancement

#317 - taxon_suggest endpoint does not return E. coli species (taxid:562)

Issue - State: open - Opened by manulera 11 months ago - 1 comment

#316 - Partial (or cached) downloads

Issue - State: closed - Opened by fgvieira 11 months ago - 1 comment
Labels: enhancement

#315 - Is there a way to get both genome and taxonomy information ?

Issue - State: closed - Opened by paulimer 11 months ago - 3 comments
Labels: enhancement

#314 - --preview option breaks download

Issue - State: closed - Opened by BioinformaticsPlatformWIV-ISP 11 months ago - 2 comments
Labels: bug

#313 - Filter of results before downloading

Issue - State: closed - Opened by fgvieira 11 months ago - 4 comments

#311 - Release updated docs for 16.4.5

Pull Request - State: closed - Opened by BradHolmes 12 months ago

#310 - Request for additional attributes for Virus Data Report

Issue - State: closed - Opened by joverlee521 12 months ago - 3 comments

#309 - Recent data missing when using `datasets download virus genome taxon`

Issue - State: closed - Opened by corneliusroemer 12 months ago - 6 comments

#308 - Release updated docs for 16.4.3

Pull Request - State: closed - Opened by BradHolmes 12 months ago

#306 - ncbi datasets cli not working (09/01/2024)

Issue - State: closed - Opened by chriswyatt1 about 1 year ago - 3 comments

#305 - Release updated docs for 16.2.0

Pull Request - State: closed - Opened by BradHolmes about 1 year ago

#304 - Download plasmids

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

#303 - Release updated docs for 16.1.1

Pull Request - State: closed - Opened by BradHolmes about 1 year ago

#302 - Include md5sum in JSON or as other output

Issue - State: open - Opened by aboffin about 1 year ago - 1 comment
Labels: checksum

#301 - incorrect length for scaffold NC_018909.1 with datasets sequence report

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

#300 - dataformat fails when provided with many fields

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

#299 - Release updated docs for 16.0.0

Pull Request - State: closed - Opened by BradHolmes about 1 year ago

#298 - --include none and --chromosomes all

Issue - State: open - Opened by conchoecia about 1 year ago - 4 comments

#297 - How can I download all bacterial genes?

Issue - State: closed - Opened by nettanetta about 1 year ago - 3 comments

#296 - server error with a large number of accessions

Issue - State: closed - Opened by jvolkening about 1 year ago - 7 comments
Labels: bug

#295 - Not all parameters of the taxonomy API work

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

#294 - Unexpected EOF Errors During Actinopterygii Genomes Download in RefSeq

Issue - State: open - Opened by mkrg01 about 1 year ago - 16 comments
Labels: bug

#293 - Release updated docs for 15.31.1

Pull Request - State: closed - Opened by BradHolmes about 1 year ago

#292 - Release updated docs for 15.31.0

Pull Request - State: closed - Opened by BradHolmes about 1 year ago

#291 - intermittent zip file issue

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

#290 - correct headers for tab-delimited output

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

#289 - OpenAPI spec not valid?

Issue - State: open - Opened by jvolkening about 1 year ago - 4 comments

#288 - Release updated docs for 15.30.0

Pull Request - State: closed - Opened by BradHolmes about 1 year ago

#287 - Cannot retrieve genome data

Issue - State: closed - Opened by gladyspoon320 about 1 year ago - 3 comments

#286 - Release updated docs for 15.28.0

Pull Request - State: closed - Opened by BradHolmes about 1 year ago

#285 - Downloading all species datasets (assembly in FASTA and annotation in GFF format) for research project

Issue - State: closed - Opened by recervictory about 1 year ago - 6 comments
Labels: question

#284 - Error: [gateway] Gateway Error (429 Too Many Requests)

Issue - State: closed - Opened by hunglin59638 about 1 year ago - 1 comment

#283 - Release updated docs for 15.27.0

Pull Request - State: closed - Opened by BradHolmes about 1 year ago

#282 - Release updated docs for 15.26.0

Pull Request - State: closed - Opened by BradHolmes about 1 year ago

#281 - can not retrieve PRJNA822777 with datasets 15.25.0

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

#280 - Issue with `summary genome taxon` and a taxon name.

Issue - State: closed - Opened by muffato about 1 year ago - 3 comments

#279 - Release updated docs for 15.25.0

Pull Request - State: closed - Opened by BradHolmes about 1 year ago

#278 - How to download paired gene mRNA-CDS-protein sequence information?

Issue - State: closed - Opened by ZYZhang17 about 1 year ago - 1 comment

#277 - Could not download virus genome

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

#275 - How to get a list of all assembly versions for a species?

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

#274 - datasets rehydrate --gzip flag does not work in release v15.23.0

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

#273 - Release updated docs for 15.23.0

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

#272 - Gogvych

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

#271 - Release updated docs for 15.21.1

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

#270 - Virus download issues

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

#269 - Release updated docs for 15.20.0

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

#268 - Query string 'filters.assembly_version'

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

#267 - Release updated docs for 15.19.0

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

#266 - Python package does not close SSL sockets.

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

#265 - Unable to download all RefSeq genomes for a single bacterial species

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

#264 - Release updated docs for 15.16.0

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

#263 - Release updated docs for 15.15.0

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

#262 - Input gene symbols are not returned in final table, request to add "input" field to dataformat

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

#261 - [feature request] Add `--assembly-version` option for virus downloads

Issue - State: closed - Opened by kapsakcj over 1 year ago - 9 comments
Labels: enhancement

#260 - runtime error: invalid memory address or nil pointer dereference - rehydrate

Issue - State: closed - Opened by krithikaarumugam over 1 year ago - 5 comments
Labels: bug

#259 - Error rename [windows]

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

#258 - Release updated docs for 15.13.0

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

#257 - Four example NCBI datasets jupyter notebooks failed to load

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

#256 - Containers for NCBI datasets

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

#255 - Release updated docs for 15.12.0

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

#253 - Large dataset download.

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

#252 - Feature request - Filter BioProject by taxon

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

#251 - Unable to download by gene symbol

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

#250 - Release updated docs for 15.10.0

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

#249 - Release updated docs for 15.9.0

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