ohmeta/metapi

A general metagenomics data mining system focus on robust microbiome research

metapi's Issues

support plasmidSPAdes

Can we support plasmidSPAdes in assembly module?

support Bandage

Navigating De novo Assembly Graphs Easily

Can we do assembly graph visualization in assembly or binning module?

without -1

metapi/metapi/rules/trimming.smk

Line 152 in 7ff5fcb

r1_str = " ".join(input[0:reads_num//2-1])

add save_host_reads option

For samples with a high ratio of host reads, the host reads maybe need to be saved for further analysis like GWAS. Is it necessary to add this option?

add deduplication option

Since fastp v0.22.0, fastp supports deduplication for FASTQ data. Specify -D or --dedup to enable this option. https://github.com/OpenGene/fastp#duplication-rate-and-deduplication
Hope you could add this option in metapi. Thanks~

Project: Manuscript

A issue to track the writing process of the manuscript.

support OPERA-MS

Long reads is comming!

Can we support hybrd assembly in assembly module?

support biosyntheticSPAdes

Can we support biosyntheticSPAdes in assembly module?

Reduce files number

1. use hd5 to store CSV file
2. remove the small file, merge to one big file, when small file update, big file update too.

conterminator

Detection of incorrectly labeled sequences across kingdoms : https://github.com/martin-steinegger/conterminator

Support PE + SE parallelly

It would be great if metapi support PE + SE assembly parallelly.

error ： r1 should be r

metapi/metapi/rules/trimming.smk

Line 225 in 66fdd5a

--thread {threads} --html {output.html} --json {output.json} 2> {log}" % r1)

metaeuk

sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics : https://github.com/soedinglab/metaeuk

Project: Documentation

We plan to make a better documentation.

Name 'directory' is not defined

I am trying to run metapi 1.1.0 under conda python 3.6.13. Using the "init" to init project seems to be fine. And when I try to execute statements like trimming or all, I got an error "name 'directory' is not defined" in the trimming.smk file.

bug report

metapi/metapi/cluster.yaml

Line 77 in 85ca61c

output: "logs/02.{rule}/{rule}.{wildcards.sample}.o"

to #L120 the output path is inconsistent with the "logs" directory.

Error: wrong header

Hi,

I have installed metapi using micromamba. Now am trying to run the code, but getting this error:

`'/pbtech_mounts/homes051/chb4004/micromamba/envs/metapi/lib/python3.11/site-packages/metapi'
wrong header: Index(['short_forward_reads', 'short_reverse_reads'], dtype='object')
Running metapi mag_wf:
snakemake --snakefile /pbtech_mounts/homes051/chb4004/micromamba/envs/metapi/lib/python3.11/site-packages/metapi/snakefiles/mag_wf.smk --configfile ./config.yaml --cores 240 --until all --rerun-incomplete --keep-going --printshellcmds --reason --use-conda --conda-prefix ~/.conda/envs --profile ./profiles/slurm --local-cores 8 --jobs 30

Real running cmd:
snakemake --snakefile /pbtech_mounts/homes051/chb4004/micromamba/envs/metapi/lib/python3.11/site-packages/metapi/snakefiles/mag_wf.smk --configfile ./config.yaml --cores 240 --until all --rerun-incomplete --keep-going --printshellcmds --reason --use-conda --conda-prefix ~/.conda/envs --profile ./profiles/slurm --local-cores 8 --jobs 30
`

I had initialized my folder using
metapi init -d . -s metapi.tsv

This is my slurm script:
`#!/bin/sh

#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=4
#SBATCH --time=168:00:00
#SBATCH --mem=25GB
#SBATCH --job-name=metapi
#SBATCH --error metapi--%j.err

micromamba shell hook -s bash
eval "$(~/bin/micromamba shell hook -s bash)"
micromamba activate metapi

metapi mag_wf all --use-conda --run-remote`

This is my sample file. The header seems to be correct based on documentation. Can you let me know what is going wrong?
Is there an example code/more documentation available?

metapi - Sheet1.csv

Long reads is comming

Everyone, long reads is comming!

Hello, nanopore and pacbio.

Need to install those software before running?

Thank you for providing such good software which can analysis the meta workflow.

when I run

metapi mag_wf all --use-conda --run-local

and I get the config.yml

Before I run the workflow ,need I download those software which in requirement? and export to the env path?

[A little feedback]

After I installed it with the command:
pip3 install metapi==2.1.1
"metapi --help" will prompt:
modulenotfounderror: no module named' seaborn'
So I need to execute the command: pip install seaborn