nextgenusfs/amptk issues and pull requests

#106 - Issues AMPtk taxonomy

Issue - State: open - Opened by msalamon2 3 months ago

#105 - VSEARCH error on amptk -filter step

Issue - State: open - Opened by MelissaIngala about 1 year ago

#104 - usearch9 not found when generate UTAX database

Issue - State: open - Opened by tangyuhua36 about 1 year ago

#103 - Error when run quick start

Issue - State: open - Opened by CourierFlag over 1 year ago - 7 comments

#102 - fix for bug #101 where qCount is None not 0

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

#100 - Issue installing AMPtk (Mac OS - M1 chip)

Issue - State: open - Opened by cpbivins28 almost 2 years ago - 2 comments

#99 - Problematic unoise3 implementation with VSEARCH

Issue - State: closed - Opened by markschl about 2 years ago - 13 comments

#98 - Saw you started some prelim ONT methods

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

#97 - Problem with TypeError during AMPtk cluster

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

#96 - unoise3 clustering

Issue - State: open - Opened by nicolereynolds1 almost 3 years ago - 5 comments

#95 - new users cannot install amptk properly, please help

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

#94 - Species names in amptk_mock2.fa and amptk_mock3.fa vs Figure 4

Issue - State: open - Opened by peterjc about 3 years ago

#93 - Bug fixes for small formatting in mock community db files.

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

#92 - fix bug #91 to support use of distro over platform in python 3.8+.

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

#91 - platform.linux_distribution is removed since Python 3.8

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

#90 - Matching MockA, MockB1 and MockB2 to FASTQ filenames

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

#89 - Inconsistent primer trimming sequence in amptk_mock*.fa

Issue - State: closed - Opened by peterjc over 3 years ago - 5 comments

#88 - Missing final new line in amptk_mock1.fa and amptk_synmock.fa

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

#87 - Missing species names in amptk_mock1.fa

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

#86 - Typo "Bjerkandara adusta" --> "Bjerkandera adusta"

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

#85 - Default for -p, --index_bleed documented as 0.005

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

#84 - SyntaxError in "duplicate ID in mapping file: XXX, exiting"

Issue - State: closed - Opened by peterjc over 3 years ago

#83 - Support Python 3.8 onwards

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

#82 - related with SynMock

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

#81 - COI Database build strips specific epithet from species column

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

#80 - Custom 16S database not found after successful installation

Issue - State: closed - Opened by JonathanVanHamme almost 4 years ago - 11 comments

#79 - amptk database error

Issue - State: closed - Opened by yuanyuan12543 about 4 years ago - 2 comments

#78 - Could not find the mydata.demux.fq.gz file after pre-processing

Issue - State: closed - Opened by yuanyuan12543 about 4 years ago - 1 comment

#77 - Arthropod database build errors in version 1.5.1 (Python 3.7)

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

#76 - Better warning/error message for demux if no primers are found

Issue - State: closed - Opened by nextgenusfs over 4 years ago

#75 - Estimate rate of index hopping consistent with amptk filter

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

#74 - Different amplicons size from BioMocks sequenced on different platforms (Illumina vs PGM).

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

#73 - ValueError: invalid literal for int() with base 10: ''

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

#72 - How to match "Zotu" to "ASV" when UNOISE3(AMPtk) generates "Zotu" while sequences in $BASE.ASVs.fa were labeled as "ASV"

Issue - State: closed - Opened by npomb001 almost 5 years ago - 1 comment

#71 - F and R primers not found, seqs not dropped?

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

#70 - OSX Catalina is 64 bit only.... thus usearch 32 bit will not run

Issue - State: closed - Opened by nextgenusfs almost 5 years ago
Labels: enhancement, question

#69 - drop UTAX from taxonomy?

Issue - State: closed - Opened by nextgenusfs almost 5 years ago - 3 comments
Labels: question

#68 - Error at Taxonomy step (ASV clustering from DADA2)

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

#67 - ValueError: could not convert string to float:

Issue - State: closed - Opened by Alenap26 almost 5 years ago - 4 comments

#66 - find_homopolymers.py

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

#65 - DADA2 Pseudopooling

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

#64 - Correct channel order

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

#63 - dada2 pipeline error

Issue - State: closed - Opened by bsmoda over 5 years ago - 6 comments

#62 - Illegal instruction: 4 - biom error?

Issue - State: closed - Opened by nicolereynolds1 over 5 years ago - 7 comments

#61 - amptk taxonomy does not create biom

Issue - State: closed - Opened by FilipeMatteoli over 5 years ago - 6 comments

#60 - DADA2 options

Issue - State: closed - Opened by mykophile over 5 years ago - 8 comments

#59 - generate fasta files from udb after database install

Issue - State: closed - Opened by hyphaltip over 5 years ago - 1 comment

#58 - UnboundLocalError: local variable 'hit' referenced before assignment when using '--fasta_db'

Issue - State: closed - Opened by Alenap26 over 5 years ago - 3 comments

#57 - Amptk summarize ValueError: not enough values to unpack (expected 2, got 1)

Issue - State: closed - Opened by Alenap26 over 5 years ago - 10 comments

#56 - UnboundLocalError: local variable 'hit' referenced before assignment when using usearch10

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

#55 - UnboundLocalError: local variable 'hit' referenced before assignment

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

#54 - change in conda install cmd

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

#53 - Illumina: Set Merge Options

Issue - State: open - Opened by Aciole-David almost 6 years ago - 2 comments

#52 - Does ion preprocessing filters only reads that contains both forward and reverse primers?

Issue - State: closed - Opened by bsmoda almost 6 years ago - 4 comments

#51 - AMPtk filter not finding usearch

Issue - State: closed - Opened by rmsegnitz almost 6 years ago - 4 comments

#50 - Does the 'amptk filter' remove non-representative OTUs ?

Issue - State: closed - Opened by bsmoda almost 6 years ago - 3 comments

#49 - centroid= not found in taxonomy dictionary

Issue - State: closed - Opened by hmontenegro almost 6 years ago - 3 comments

#48 - amptk summarize

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

#47 - update citation link in docs

Issue - State: closed - Opened by nextgenusfs about 6 years ago

#46 - 16s Illumina

Issue - State: closed - Opened by FilipeMatteoli about 6 years ago - 8 comments

#45 - amptk v1.2.5 taxonomy error

Issue - State: closed - Opened by AlexGaithuma about 6 years ago - 4 comments

#44 - add SILVA/greengenes DB to 16S amptk taxonomy

Issue - State: open - Opened by nextgenusfs over 6 years ago - 11 comments
Labels: enhancement

#43 - a little quirk (bug?) due to formatting in `biom convert`

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

#42 - install question

Issue - State: closed - Opened by devonorourke over 6 years ago - 18 comments

#41 - Appending Taxonomy Error

Issue - State: closed - Opened by MycoMap over 6 years ago - 4 comments

#40 - Building new Arthropod database: novice troubles

Issue - State: closed - Opened by JonathanVanHamme over 6 years ago - 26 comments

#39 - Auto-detection of output base name error

Issue - State: closed - Opened by nextgenusfs almost 7 years ago - 1 comment

#38 - Combining multiple Ion chip runs

Issue - State: closed - Opened by JonathanVanHamme almost 7 years ago - 4 comments

#37 - Python3

Pull Request - State: closed - Opened by nextgenusfs almost 7 years ago

#36 - something funny...

Issue - State: closed - Opened by devonorourke almost 7 years ago - 4 comments

#35 - feature request for 'amptk filter'

Issue - State: closed - Opened by devonorourke almost 7 years ago - 8 comments

#34 - Nanopore

Issue - State: open - Opened by devonorourke about 7 years ago - 11 comments

#33 - amptk taxonomy help menu for `-i` argument

Issue - State: closed - Opened by devonorourke about 7 years ago - 2 comments

#32 - tiny request on database/taxonomy install

Issue - State: closed - Opened by devonorourke about 7 years ago - 4 comments
Labels: enhancement

#31 - amptk filter --subtract functionality

Issue - State: closed - Opened by devonorourke about 7 years ago - 13 comments

#30 - hiseq vs. miseq output mixup?

Issue - State: closed - Opened by devonorourke about 7 years ago - 9 comments

#29 - amptk filter - structure of otutable.demux.fq for new OTU table

Issue - State: closed - Opened by jack1120 about 7 years ago - 3 comments

#28 - Changed files using best practices to reduce number of image layers

Pull Request - State: closed - Opened by strund3r over 7 years ago

#27 - Hybrid taxonomy abbreviations

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

#26 - amptk-extract_region.py - 'newtaxLen' is not defined

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

#25 - edlib - invalid ELF header

Issue - State: closed - Opened by vmikk over 7 years ago - 3 comments

#24 - Reference database updates & Wiki

Issue - State: closed - Opened by vmikk over 7 years ago - 11 comments

#23 - Update README.md

Pull Request - State: closed - Opened by hyphaltip almost 8 years ago - 1 comment

#22 - Results naming for DADA2 and UNOISE2

Issue - State: closed - Opened by vmikk almost 8 years ago - 3 comments

#21 - totally not a big issue, but perhaps something that could help?

Issue - State: closed - Opened by devonorourke about 8 years ago - 2 comments

#20 - Amptk merge

Pull Request - State: closed - Opened by nextgenusfs about 8 years ago

#19 - Composition of each OTU?

Issue - State: closed - Opened by nextgenusfs about 8 years ago - 6 comments
Labels: enhancement

#18 - Mock Communities

Issue - State: closed - Opened by MycoMap about 8 years ago - 2 comments

#17 - UFITS Summarize

Issue - State: closed - Opened by MycoMap about 8 years ago - 4 comments

#16 - trivial doc typo

Pull Request - State: closed - Opened by hyphaltip about 8 years ago

#15 - missing vsearch for the R2 fastq_filter reads

Pull Request - State: closed - Opened by hyphaltip about 8 years ago - 1 comment

#14 - RDP run ends with crash

Issue - State: closed - Opened by hyphaltip about 8 years ago - 2 comments

#13 - usearch9 multithread fastq_filter is crashing

Issue - State: closed - Opened by hyphaltip about 8 years ago - 3 comments

#12 - Mock Community Question

Issue - State: closed - Opened by MycoMap over 8 years ago - 7 comments

#11 - ufits cluster

Issue - State: closed - Opened by MycoMap over 8 years ago - 2 comments

#10 - Illumina Processing results in zero sequences

Issue - State: closed - Opened by MycoMap over 8 years ago - 4 comments

#9 - brew install ufits zlib issue

Issue - State: closed - Opened by cour10eygrace over 8 years ago - 8 comments

#8 - CSV vs TSV OTU tables in ufits taxonomy command

Issue - State: closed - Opened by nextgenusfs over 8 years ago - 1 comment
Labels: bug, enhancement

#7 - ufits taxonomy: make OTU table optional

Issue - State: closed - Opened by vmikk over 8 years ago - 3 comments
Labels: enhancement

#6 - add psutil to dependencies

Pull Request - State: closed - Opened by vmikk over 8 years ago - 1 comment

GitHub / nextgenusfs/amptk issues and pull requests