Ecosyste.ms: Issues

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

GitHub / WrightonLabCSU/DRAM issues and pull requests

#298 - Error when setting up databases

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

#297 - Permission error when setting up databases

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

#296 - default prodigal command request

Issue - State: open - Opened by bck243 over 1 year ago

#295 - Errno 13

Issue - State: open - Opened by Valentin-Bio over 1 year ago

#294 - ValueError: duplicate headers in DRAM-v.py but not when running DRAM.py

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

#293 - scikit-bio release 0.5.9 brings up ImportError.

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

#292 - testing database

Issue - State: closed - Opened by fujch7 over 1 year ago

#291 - description_db.sqlite is taking extremely long to write

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

#290 - Correct syntax for the program "DRAM.py merge_annotations"

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

#289 - KeyError: 'amg_database' in DRAM-v

Issue - State: open - Opened by nologo68 over 1 year ago - 2 comments

#288 - amg_flags - glossary?

Issue - State: closed - Opened by GeoMicroSoares over 1 year ago

#287 - DRAM distill output errors: almost all values are zeros

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

#286 - DRAM-v.py --low_mem_mode breaks distill

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

#284 - Is --gene_ko_link_loc necessary if I used --kegg_loc ?

Issue - State: closed - Opened by mol529 over 1 year ago - 1 comment

#282 - cp12 identification

Issue - State: open - Opened by Drob84761 over 1 year ago - 1 comment

#281 - object has no attribute query error

Issue - State: open - Opened by saras224 over 1 year ago

#280 - download database step is extremely slow

Issue - State: open - Opened by jianshu93 over 1 year ago - 2 comments

#279 - Any way to reorganize the distill heatmap

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

#278 - DRAM-v.py annotate

Issue - State: open - Opened by Altay88 over 1 year ago

#277 - Error while annotating MAGs

Issue - State: open - Opened by saras224 over 1 year ago - 1 comment

#276 - DRAM how to provide database location

Issue - State: open - Opened by saras224 almost 2 years ago

#275 - VOG annotations Description_Db_Updated: Unknown, or Never

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

#274 - Bottleneck in database download-reg

Issue - State: open - Opened by srisvs33 almost 2 years ago

#273 - KEGG reformatting regarding to #182

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

#272 - DRAM-v databases

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

#271 - 155796 killed

Issue - State: open - Opened by TKsh6 almost 2 years ago - 9 comments

#270 - error with DRAM-v distill

Issue - State: open - Opened by Qiqi04Tsinghua almost 2 years ago - 4 comments

#269 - Errors about summariziung anntotations

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

#268 - Resume database setup after error?

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

#267 - DRAM2 to spot unexpected combo?

Issue - State: open - Opened by Kirk3gaard almost 2 years ago

#266 - DRAM_product_annotations

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

#265 - Database prep issues

Issue - State: closed - Opened by dnolin13 almost 2 years ago

#264 - Issue in database setup

Issue - State: closed - Opened by dnolin13 almost 2 years ago - 2 comments

#263 - Problem during prepare the database

Issue - State: open - Opened by Gu2uMo about 2 years ago - 15 comments

#260 - dbCAN

Issue - State: open - Opened by JoseLopezArcondo about 2 years ago - 10 comments

#257 - Add workflow for linear api

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

#255 - Push a point release to react to ref-seqs changes

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

#254 - URLopen error

Issue - State: closed - Opened by spencerlong1 about 2 years ago - 12 comments
Labels: bug

#253 - "Present in contig" in dramv distill product heatmap

Issue - State: open - Opened by ereyred about 2 years ago - 1 comment

#252 - Apparently you are using only the best hit for CAZy . is there a better option?

Issue - State: open - Opened by SilasK about 2 years ago - 2 comments

#251 - Regarding Viral AMG classification

Issue - State: open - Opened by ShailNair about 2 years ago - 11 comments
Labels: enhancement, question

#246 - README.md: Direct installation from bioconda

Pull Request - State: closed - Opened by wwood about 2 years ago - 1 comment

#245 - Error in Getting hits from dbCAN

Issue - State: closed - Opened by dgittins about 2 years ago - 6 comments
Labels: bug

#244 - Fixing a bug in setup

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

#243 - error with DRAM-setup.py prepare_databases

Issue - State: closed - Opened by DrYoungOG about 2 years ago - 6 comments

#242 - DRAM-setup.py prepare_databases issue

Issue - State: closed - Opened by YilingWang1997 about 2 years ago - 2 comments

#241 - Fix loc bug

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

#240 - DRAM-setup.py set_database_locations issue

Issue - State: closed - Opened by dgittins about 2 years ago - 8 comments
Labels: bug

#239 - Fix loc bug

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

#238 - Eukaryotic MAGs/assemblies

Issue - State: open - Opened by andressamv about 2 years ago - 2 comments
Labels: question

#237 - DRAM distill: AttributeError: 'Series' object has no attribute 'Note'

Issue - State: closed - Opened by Cam-Baker about 2 years ago - 6 comments

#236 - Issue with downloading viral database (DRAM version 1.4.0)

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

#235 - Can I download the database manually?

Issue - State: closed - Opened by chengzhongyi8 about 2 years ago - 1 comment

#234 - Will DRAM-v also work on non-phage viruses like NCLDV?

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

#233 - DRAM annotate_genes

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

#232 - DRAM hanging on Merging ORF annotations step

Issue - State: closed - Opened by Rridley7 over 2 years ago - 7 comments
Labels: enhancement

#231 - DRAM.py merge_annotations error, not recognizing argument

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

#230 - whether I have successfully set up the dram database?

Issue - State: closed - Opened by Sautumn-Lin over 2 years ago

#228 - Improved amg summary

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

#227 - DRAM.py annotate stops at "Getting hits from pfam"

Issue - State: closed - Opened by alyzza16 over 2 years ago - 7 comments

#226 - Memory limitations

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

#225 - DRAM.py error message for tRNAscan-SE

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

#224 - `DRAM-setup.py set_database_locations --update_description_db` process was Killed

Issue - State: closed - Opened by HushKuo over 2 years ago - 9 comments

#223 - Error in DRAM-setup.py with snakemake

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

#222 - Error at "Getting descriptions of hits from peptidase" step

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

#221 - DRAM database setup fails even after skipping Uniref

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

#220 - AttributeError: 'NoneType' object has no attribute 'query' in Dram 1.3.5

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

#219 - No information for some AMGs

Issue - State: closed - Opened by chenyj8 over 2 years ago - 3 comments

#218 - About the viral gene flags "K" and "E" from DRAM-v

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

#217 - Question about implementation of Pfam

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

#216 - Dram database download issue looking for files with previous datestamps

Issue - State: closed - Opened by jayramr over 2 years ago - 6 comments

#215 - DB can v11 was just released

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

#214 - Wiki link to 404

Issue - State: closed - Opened by cmkobel over 2 years ago - 2 comments
Labels: bug

#213 - -o option should have argument `required=True`

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

#212 - database_handler.py:51: UserWarning: Database does not exist at path None

Issue - State: closed - Opened by cmkobel over 2 years ago - 16 comments

#211 - DRAM-v Annotate Called Genes

Issue - State: closed - Opened by chenyj8 over 2 years ago - 1 comment

#208 - DRAM database config should be accessible / configurable by users

Issue - State: closed - Opened by gregvonkuster over 2 years ago - 6 comments

#207 - Dram1.4rc

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

#206 - Change all FTP URLs to HTTP(s) to avoid firewall/ACL issues

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

#203 - Pathway Tools compatible genbank file

Issue - State: open - Opened by kebow over 2 years ago - 2 comments
Labels: enhancement, help wanted, good first issue

#201 - Add ability to set location of config file

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

#200 - Unable to view heatmap

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

#199 - KeyError

Issue - State: closed - Opened by woodoo46 over 2 years ago - 10 comments

#197 - Scikit fix

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

#196 - DRAM issue with setting up databases

Issue - State: closed - Opened by yugen-miyahara over 2 years ago - 13 comments

#191 - Scipy error while downloading the databases

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

#188 - DRAM error while annotation

Issue - State: closed - Opened by poddarharsh15 over 2 years ago - 11 comments

#182 - How to prepare a single .pep KEGG database for DRAM database setup step

Issue - State: closed - Opened by nixon444 over 2 years ago - 5 comments

#177 - A question about viral hallmark gene and viral-like gene

Issue - State: open - Opened by fanlu-f almost 3 years ago - 2 comments
Labels: question

#176 - KeyError vogdb categories

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

#171 - DRAM-setup.py prepare_databases --skip_uniref produces error

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

#169 - All code 3.6 compatible, dbcan description test

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

#162 - InvalidIndexError: Reindexing only valid with uniquely valued Index objects

Issue - State: closed - Opened by michoug almost 3 years ago - 10 comments

#160 - Is there a way to predict if a genome is anaerobic / (factultative) aerobic?

Issue - State: open - Opened by SilasK almost 3 years ago - 1 comment
Labels: question

#158 - No descriptions were found for your IDs error

Issue - State: closed - Opened by MaxRubinBlum almost 3 years ago - 27 comments