amptk

amptk copied to clipboard

Error when run quick start

7

I was learning amptk, and ran AMPtk Quick Start guidling to process test data from and I got this error when filtering. ################ Traceback (most recent call last): File "/home/user1/miniconda3/envs/amptk154/bin/amptk",...

CourierFlag

Hello, I am using amptk to analyze some paired-end COI diet data from bat feces. I have mostly gotten the pipeline to work, except for the amptk -filter step. My...

MelissaIngala

When I tried to build custom COI database,I got this error in step #generate UTAX database ##########this is my code amptk database -i arth10000.BIN-consensus.fasta -f LCO1490 -r GGWACTAATCAATTTCCAAATCC --primer_required rev...

tangyuhua36

Getting this error ``` Traceback (most recent call last): File "/opt/linux/rocky/8.x/x86_64/pkgs/amptk/1.6/bin/amptk", line 8, in sys.exit(main()) File "/bigdata/operations/pkgadmin/opt/linux/centos/8.x/x86_64/pkgs/amptk/1.6/lib/python3.10/site-packages/amptk/amptk.py", line 784, in main mod.main(arguments) File "/bigdata/operations/pkgadmin/opt/linux/centos/8.x/x86_64/pkgs/amptk/1.6/lib/python3.10/site-packages/amptk/OTU_cluster.py", line 190, in main numKept, numDropped...

hyphaltip

Issue installing AMPtk (Mac OS - M1 chip)

2

Hi, I'm currently unable to successfully install AMPtk. Following the installation instructions on https://amptk.readthedocs.io/en/latest/ - I type in the first three commands: conda config --add channels defaults conda config --add...

cpbivins28

add SILVA/greengenes DB to 16S amptk taxonomy

11

problem is reformatting the taxonomy information in format needed by UTAX/SINTAX. I've previously looked at SILVA taxonomy -- the taxonomy appeared to be a hot mess (I'm not a bacteriologist).......

nextgenusfs

unoise3 clustering

5

I am trying to cluster my data using unoise3 with the following command: amptk unoise3 -i out_lr22.demux.fq.gz -o out_lr22 -p 98 -e 2.0 --usearch usearch10 I know usearch is no...

nicolereynolds1

Saw you started some prelim ONT methods

2

I have some sets of dual indexed fungal ITS amplicon pools from specimens. One is 288 specimens and the other is 480 specimens if they would be helpful at all...

MycoMap

new users cannot install amptk properly, please help

3

Hi there, I am new to this package, when I try to install amptk from conda, I had no luck.. could anyone help me? Thanks in advance. First, I created...

SihaoC

Cross reference #87, ``amptk_mock1.fa`` was earlier work and does not have species names. Pulling out the species names, ``` $ grep "^>" amptk_mock[2-3].fa | cut -f 2 -d ">" |...

peterjc