picrust / picrust2

Code, unit tests, and tutorials for running PICRUSt2

picrust/picrust2 Issues

Please help for picrust2 tutorial: cannot download the data set
Closed a month ago4
complex definition effect on abundance calculation
Updated 2 months ago
During pytest place_seqs.py fails and cannot run the full pipeline
Updated 2 months ago5
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x89 in position 0: invalid start byte
Closed 2 months ago3
Gene family abundances per ASV rather than per sample
Closed 2 months ago1
PICRTUST 2 No such file or directory: 'hmmalign'
Closed 2 months ago2
Assign general function from KEGG pathway in pathways_out
Closed 2 months ago1
Macbook M1 chip pytest error (sqlite3 import??)
Updated 2 months ago1
pytest fails 1 test on test_place_seqs.py
Closed 2 months ago2
Absolute abundance data for picrust2
Updated 3 months ago2
Error runnig picrust due to cannot import name '_convert_node_to_root_polytomy'
Updated 2 months ago1
Running picrust on shotgun output from bracken
Closed 2 months ago2
metagenome contributions analysis
Closed 2 months ago2
running picrust2 on ITS
Closed 2 months ago2
Customize database guidance
Updated 4 months ago3
Question about previous filtering of otu table
Closed 2 months ago3
maximum recursion depth exceeded while calling a Python object
Closed 6 months ago
help please : Error running picrust2_pipeline.py
Closed 2 months ago2
Installing problem into MacBook Air m1 terminal
Updated 2 months ago8
tests/test_place_seqs.py shows failed status upon running the 'pytest' command
Closed 2 months ago3
Is not like an issue but more like an aha moment
Closed 2 months ago3
picrust2_outputs
Closed 2 months ago2
picrust2 installation
Closed 2 months ago3
PicRust2 Error : number of statistically significant pathways exceeds the database's query limit.
Closed 2 months ago5
Error in Picrust2_pipeline.py
Closed 2 months ago2
clarification on path_abun_contrib - contributory bacteria to metabolic profile
Closed 7 months ago1
metagenome_pipeline.py - flag to reduce amount of memory used
Closed 2 months ago2
Issue with using picrust2 pipeline for ITS sequences
Closed 2 months ago2
Does PiCrust2 generate 16S taxonomic classifications using your reference tree?
Closed 2 months ago3
Error with hsp.py step with tutorial data
Closed 10 months ago3
Analyzing Oxford Nanopore 16s data with Picrust2
Closed 2 months ago2
3,751 input sequences aligned poorly to reference sequences and removed.
Closed 2 months ago2
de-novo clustered ASVs as input sequences in picrust2
Closed 2 months ago2
how long should full pipeline command run?
Closed 2 months ago2
Error of running picrust2_pipeline
Updated 2 months ago4
biom-format not found
Closed 2 months ago4
How to use a custom KEGG database?
Closed 2 months ago1
pytest fails tests/test_place_seqs.py
Updated 2 months ago4
issue downloading Picrust
Closed a year ago
object 'p_values_df' not found (error)
Closed 2 months ago2
Requirement for fasta sequences and questions for when using Nanopore 16S data
Closed 2 months ago1
Question about the methods of Hidden-state prediction
Closed 2 months ago1
Command error about picrust2 ?
Closed 2 months ago2
Question about Taxonomic info
Closed 2 months ago2
add_descriptions.py does not work for stratified file
Updated a year ago2
MemoryError
Closed 2 months ago4
what is the mean of the column name“taxon_rel_abun/genome_function_count/taxon_function_abun/taxon_rel_function_abun” in the KEGG_pathways_out/path_abun_contrib.tsv.gz/path_abun_contrib.tsv
Closed 2 months ago1
File "pandas/_libs/parsers.pyx", line 1973, in pandas._libs.parsers.raise_parser_error pandas.errors.ParserError: Error tokenizing data. C error: EOF inside string starting at row 37
Closed 2 months ago3
Error in running epa-ng
Closed 2 months ago2
Error with epa-ng
Closed 2 months ago2