This is my first time using nf-core/viralrecon. When trying to run the command with my data I got the error
-- Check script '/home/joancuesta/.nextflow/assets/nf-core/viralrecon/./workflows/illumina.nf' at line: 26 or see '.nextflow.log' file for more details
Could you please help me?
Command used and terminal output
Command used:
nextflow run nf-core/viralrecon --input rv3471.csv --platform illumina --protocol metagenomic --outdir /home/joancuesta/quasispecies/3471 --fasta KX148107.fasta --skip_nextclade -profile docker
Terminal output:
N E X T F L O W ~ version 23.10.1
Launching `https://github.com/nf-core/viralrecon` [drunk_laplace] DSL2 - revision: 3731dd3a32 [master]
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,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/viralrecon v2.6.0-g3731dd3
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Core Nextflow options
revision : master
runName : drunk_laplace
containerEngine: docker
launchDir : /home/joancuesta/quasispecies
workDir : /home/joancuesta/quasispecies/work
projectDir : /home/joancuesta/.nextflow/assets/nf-core/viralrecon
userName : joancuesta
profile : docker
configFiles : /home/joancuesta/.nextflow/assets/nf-core/viralrecon/nextflow.config
Input/output options
input : rv3471.csv
platform : illumina
protocol : metagenomic
outdir : /home/joancuesta/quasispecies/3471
Reference genome options
fasta : KX148107.fasta
Nanopore/Illumina options
skip_nextclade : true
!! Only displaying parameters that differ from the pipeline defaults !!
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If you use nf-core/viralrecon for your analysis please cite:
* The pipeline
https://doi.org/10.5281/zenodo.3901628
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/viralrecon/blob/master/CITATIONS.md
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-- Check script '/home/joancuesta/.nextflow/assets/nf-core/viralrecon/./workflows/illumina.nf' at line: 26 or see '.nextflow.log' file for more details
Nextflow version (23.10.1)
Hardware (x86_64)
Executor (awsbatch)
Container engine: (Docker)
OS (Linux #61~20.04.1-Ubuntu)
Version of nf-core/viralrecon (v2.6.0-g3731dd3)
Description of the bug
This is my first time using nf-core/viralrecon. When trying to run the command with my data I got the error -- Check script '/home/joancuesta/.nextflow/assets/nf-core/viralrecon/./workflows/illumina.nf' at line: 26 or see '.nextflow.log' file for more details Could you please help me?
Command used and terminal output
Relevant files
.nextflow.log
System information
Nextflow version (23.10.1) Hardware (x86_64) Executor (awsbatch) Container engine: (Docker) OS (Linux #61~20.04.1-Ubuntu) Version of nf-core/viralrecon (v2.6.0-g3731dd3)