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GitHub / picrust/picrust2 issues and pull requests

#322 - Issue with using picrust2 pipeline for ITS sequences

Issue - State: open - Opened by dixi06 almost 2 years ago

#320 - Error with hsp.py step with tutorial data

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

#319 - Analyzing Oxford Nanopore 16s data with Picrust2

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

#318 - 3,751 input sequences aligned poorly to reference sequences and removed.

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

#317 - de-novo clustered ASVs as input sequences in picrust2

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

#316 - how long should full pipeline command run?

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

#315 - Error of running picrust2_pipeline

Issue - State: open - Opened by Gahyeon-Baek about 2 years ago - 3 comments

#314 - biom-format not found

Issue - State: open - Opened by Nazzy87 about 2 years ago - 1 comment

#313 - How to use a custom KEGG database?

Issue - State: open - Opened by BenWu1224 about 2 years ago - 1 comment

#312 - pytest fails tests/test_place_seqs.py

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

#311 - issue downloading Picrust

Issue - State: closed - Opened by mrgambero about 2 years ago

#310 - object 'p_values_df' not found (error)

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

#308 - Question about the methods of Hidden-state prediction

Issue - State: open - Opened by Teo2091 about 2 years ago - 1 comment

#307 - Command error about picrust2 ?

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

#306 - Question about Taxonomic info

Issue - State: open - Opened by 21312zhy about 2 years ago - 2 comments

#305 - add_descriptions.py does not work for stratified file

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

#304 - MemoryError

Issue - State: open - Opened by qbdong122 over 2 years ago - 4 comments

#301 - Error in running epa-ng

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

#300 - 2.5.2

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

#299 - Error with epa-ng

Issue - State: open - Opened by yliu3089 over 2 years ago - 1 comment

#298 - pathway_pipeline.py operation failed on a column

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

#297 - Missing default_files

Issue - State: closed - Opened by stevens-1 over 2 years ago - 4 comments

#296 - Missing metacyc nitrogen pathways?

Issue - State: closed - Opened by kaw97 over 2 years ago - 2 comments

#295 - q2-picrust2-2021.11_0 will not install with qiime 2023.2

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

#293 - PICRUSt2 Data and STAMP

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

#291 - q2-picrust2 Tutorial error_ "pro_ref.raxml_info" could not be found.

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

#290 - Getting Reverse Complementary Seqs

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

#289 - Calling in ITS reference

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

#288 - Running PICRUSt on ITS sequences

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

#287 - Unable to install v2.5.1 on MackBook M1 with Monterey

Issue - State: open - Opened by borexino over 2 years ago - 13 comments

#286 - warning line 341 "metagenome_pipeline.py"

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

#285 - v2.5.1

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

#284 - PICRUSt2 with other database(e.g. cowpi)

Issue - State: closed - Opened by sangmok920622 almost 3 years ago - 2 comments

#283 - Invalid model name error

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

#281 - Error picrust2 picrust2_pipeline.py

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

#280 - Retrieving more Fungi genomes for ITS and 18S predictions

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

#279 - COG3512 was eliminated in the latest COG database (2020)

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

#278 - Error in runing picrust 2

Issue - State: closed - Opened by linki11 almost 3 years ago - 2 comments

#277 - FutureWarning / deprecation warnings

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

#276 - place_seqs.py --ref_dir questions

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

#275 - Generating a KEGG module table from the KO table

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

#274 - Error in predicting functions using fungal ITS data

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

#273 - UserWarning: A worker stopped while some jobs were given to the executor.

Issue - State: closed - Opened by YuZhang-learner almost 3 years ago - 15 comments

#272 - PICRUST2 for ITS

Issue - State: closed - Opened by weibokong27 almost 3 years ago - 2 comments

#271 - mamba env create -f picrust2-env.yaml error

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

#270 - Standard error of the above failed command

Issue - State: closed - Opened by TKsh6 almost 3 years ago - 4 comments

#268 - add_description workflow in metacyc (similar to KEGG)?

Issue - State: closed - Opened by marwa38 almost 3 years ago - 1 comment

#266 - Missing almost all OTUs from marker_predicted_and_nsti.tsv.gz

Issue - State: closed - Opened by lauramason326 about 3 years ago - 9 comments

#265 - PPICRUSt2 in Galaxy

Issue - State: closed - Opened by george-weingart about 3 years ago

#264 - _queue.Empty: parallel.py", line 822, in dispatch_one_batch

Issue - State: closed - Opened by george-weingart about 3 years ago - 3 comments

#263 - Stopping - no sequence ids overlap between all three of the input files.

Issue - State: closed - Opened by Valentin-Bio-zz about 3 years ago - 1 comment

#262 - R versions mismatch

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

#261 - correct pvalues for the inferred pathways?

Issue - State: closed - Opened by marwa38 about 3 years ago - 1 comment

#257 - Guidance on how to develop a custom trait table

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

#256 - May seem like a silly question, but how do I access the output files?

Issue - State: closed - Opened by chuynh96 about 3 years ago - 2 comments

#255 - q2-picrust2 do not produce output file but no error reported

Issue - State: closed - Opened by wangyd666 about 3 years ago - 6 comments

#254 - interpretation of superpathway and pathways

Issue - State: closed - Opened by jazberna1 about 3 years ago - 3 comments

#253 - Pathway Abundance per sample vs KO abundance per sample

Issue - State: closed - Opened by Lor-AM over 3 years ago - 4 comments

#252 - v2.5.0 update

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

#251 - KEGG description for KO ids

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

#250 - Error in Installing Picrust2

Issue - State: closed - Opened by carlmed00 over 3 years ago - 1 comment

#249 - An error occurred with the pytest command

Issue - State: closed - Opened by xmcr over 3 years ago - 4 comments

#247 - place_seqs.py -s isnt getting executed

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

#246 - Picrust2 Pytest Issue

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

#245 - Understanding pathway_pipeline.py

Issue - State: closed - Opened by carlmed00 over 3 years ago - 1 comment

#243 - find ASVs' weights for each pathway

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

#241 - Minpath version

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

#236 - KO_pred_metagenome_unstrat into KEGG pathways (parent or level 2)?

Issue - State: closed - Opened by marwa38 over 3 years ago - 2 comments

#235 - Interpretation of metacyc superpathways

Issue - State: closed - Opened by andrewd789 over 3 years ago - 3 comments

#234 - Interpreting shuffled predictions

Issue - State: closed - Opened by msmcfarlin over 3 years ago - 9 comments

#233 - ASVs poorly aligned?

Issue - State: closed - Opened by marwa38 over 3 years ago - 1 comment

#232 - all the sequences are aligned poorly to reference sequences ones

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

#230 - Error: No objects to concatenate

Issue - State: closed - Opened by Biancabrown over 3 years ago - 6 comments

#228 - correcting dependencies after running `pytest`

Pull Request - State: closed - Opened by valentynbez over 3 years ago - 1 comment

#227 - pytest failure tests/test_place_seqs.py

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

#226 - Question on ASV placement

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

#225 - pathway_pipeline.py error

Issue - State: closed - Opened by ksong4 over 3 years ago - 4 comments

#224 - Error in inputs files

Issue - State: closed - Opened by mafbio over 3 years ago - 4 comments

#223 - Error using custom-map-table

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

#222 - Several modules in "KEGG_modules_to_KO.tsv" have no descriptions

Issue - State: closed - Opened by wangpeng407 over 3 years ago - 3 comments

#216 - Collapsing Metacyc pathways in the pathway abundance file

Issue - State: closed - Opened by Georgie-ru over 3 years ago - 4 comments

#215 - Picrust2 pipeline problem

Issue - State: closed - Opened by Lin1111111111 over 3 years ago - 8 comments

#213 - Databases update tutorial

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

#212 - pathway_pipeline.py killed

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

#211 - Integrating the picrust2 into usegalaxy

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

#207 - Representation of environments

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