NanoPlot: error: arguments required + command not found

[ccerpas]

Hi I can not use nanoplot to run my sequences QC. After installed with conda, I received this massage NanoPlot: error: one of the arguments --fastq --fasta --fastq_rich --fastq_minimal --summary --bam --ubam --cram --pickle --feather is required I updated using: pip install NanoPlot –upgrade and got this; Successfully uninstalled NanoPlot-1.32.1 Successfully installed NanoPlot-1.40.0 Python-Deprecated-1.1.0 kaleido-0.2.1 but I got the same deal then I tried conda update nanoplot

when I run my QC I received the next message: nanoplot: command not found

Thanks for any help you can give me, I'm a newbie at this.

[wdecoster]

Hi,

Please add the commands that you tried.

Wouter

[ccerpas]

Hi, thanks for your quick answer. I used conda create --name nanoplot conda update -n base -c defaults conda conda activate nanoplot conda install -c biconda nanoplot at this point I get the next message: Collecting package metadata (current_repodata.json): failed

UnavailableInvalidChannel: The channel is not accessible or is invalid. channel name: biconda channel url: https://conda.anaconda.org/biconda error code: 404

You will need to adjust your conda configuration to proceed. Use conda config --show channels to view your configuration's current state, and use conda config --show-sources to view config file locations.

I ran those last two without changing anything (there was no option), configuration was - defaults and the sources shows nothing

then NanoPlot with no good results (command not found) then I tried with conda install -c bioconda/label/cf201901 nanoplot but also fails solving the environments

[wdecoster]

conda install -c biconda nanoplot

It's bioconda. not biconda.

Try this:

conda create -n nanoplot nanoplot
conda activate nanoplot
NanoPlot -h

[ccerpas]

Hi, I'm still having the problem when I run the NanoPlot -h command everything looks fine, but then, when I run the nanoplot analysis I'm still having the argument require error than I mentioned before.

[wdecoster]

I can't help you if you don't share the command you tried.

[lucyintheskyzzz]

Hi I am getting the same error message, which is weird because I used the same code I used a few days ago:

!/bin/bash

SBATCH -A loni_virus2023 ### Allocation name

SBATCH -p single ## queue name

SBATCH -t 2:00:00 ## wall time

SBATCH -N 1 ## number of nodes

SBATCH -n 16 ## number of tasks

SBATCH -c 47 ## number of cores per task

SBATCH -o nanoplot.out ## standard output file

SBATCH -e nanoplot.err ## standard error file

SBATCH --mail-type FAIL

SBATCH --mail-type BEGIN

SBATCH --mail-type END

SBATCH --mail-user kvigil@tulane.edu

SBATCH -J nanoplot_seawater ## job name

activate conda

source /usr/local/packages/python/3.9.7-anaconda/etc/profile.d/conda.sh

Load the Nanoplot module

conda activate nanoplot-env

NanoPlot 1.32.1 version

Define the directory containing FASTQ files

fastq_dir="/work/kvigil/ONR020124_oyster/concatenate/concatenate"

Define the output directory for Nanoplot results

output_dir="${fastq_dir}/nanoplot_results"

Create the Nanoplot results directory if it doesn't exist

mkdir -p "$output_dir"

Iterate over all FASTQ files in the directory

for fastq_file in "${fastq_dir}"/*.fastq.gz; do

Check if the current file is a regular file

if [[ -f "$fastq_file" ]]; then
    # Run Nanoplot on the current FASTQ file
    NanoPlot -t 48 -o "${output_dir}/$(basename ${fastq_file%.fastq.gz})" "$fastq_file"
fi

done

error message from log file: usage: NanoPlot [-h] [-v] [-t THREADS] [--verbose] [--store] [--raw] [--huge] [-o OUTDIR] [-p PREFIX] [--tsv_stats] [--maxlength N] [--minlength N] [--drop_outliers] [--downsample N] [--loglength] [--percentqual] [--alength] [--minqual N] [--runtime_until N] [--readtype {1D,2D,1D2}] [--barcoded] [--no_supplementary] [-c COLOR] [-cm COLORMAP] [-f {eps,jpeg,jpg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff}] [--plots [{kde,hex,dot,pauvre} [{kde,hex,dot,pauvre} ...]]] [--listcolors] [--listcolormaps] [--no-N50] [--N50] [--title TITLE] [--font_scale FONT_SCALE] [--dpi DPI] [--hide_stats] (--fastq file [file ...] | --fasta file [file ...] | --fastq_rich file [file ...] | --fastq_minimal file [file ...] | --summary file [file ...] | --bam file [file ...] | --ubam file [file ...] | --cram file [file ...] | --pickle pickle | --feather file [file ...]) NanoPlot: error: one of the arguments --fastq --fasta --fastq_rich --fastq_minimal --summary --bam --ubam --cram --pickle --feather is required

[wdecoster]

NanoPlot: error: one of the arguments --fastq --fasta --fastq_rich --fastq_minimal --summary --bam --ubam --cram --pickle --feather is required