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Setup fails, complaining about inability to create a subfolder (vibrant) in the folder I supply with the --db argument. Without custom --db works fine, but I don't want the databases to be in my home folder.
Command used and terminal output
Without sudo:
N E X T F L O W ~ version 23.04.3
Launching `https://github.com/deng-lab/viroprofiler` [tender_austin] DSL2 - revision: c2a1f1871b [main]
----------------------------------------------------------------------------------------------------------------
__
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`888. .8' `"' 88 ss 88 888 `" `"' `888
`888. .8' oooo oooo d8b .ooooo. 88__88 oooo d8b .ooooo. o888oo oooo 888 .ooooo. oooo d8b
`888. .8' `888 `888""8P d88' `88b || `888""8P d88' `88b 888 `888 888 d88' `88b `888""8P
`888.8' 888 888 888 888 _||_ 888 888 888 888 888 888 888ooo888 888
`888' 888 888 888 888 // || \\ 888 888 888 888 888 888 888 .o 888
`8' o888o d888b `Y8bod8P' // \\ d888b `Y8bod8P' o888o o888o o888o `Y8bod8P' d888b
ViroProfiler v0.2.4
----------------------------------------------------------------------------------------------------------------
Core Nextflow options
revision : main
runName : tender_austin
containerEngine: singularity
launchDir : /media/bioinf/Data/viroprofiler
workDir : /media/bioinf/Data/viroprofiler/work
projectDir : /home/bioinf/.nextflow/assets/deng-lab/viroprofiler
userName : bioinf
profile : singularity
configFiles : /home/bioinf/.nextflow/assets/deng-lab/viroprofiler/nextflow.config
Input/output options
mode : setup
db : /media/bioinf/Data/viroprofiler
outdir : output
QC
contamref_idx : /home/bioinf/viroprofiler/contamination_refs/hg19/ref
Contig library parameters
assemblies : scaffolds
Others
use_iphop : true
use_dram : true
Max job request options
max_cpus : 1
max_memory : 8.GB
max_time : 12.h
!! Only displaying parameters that differ from the pipeline defaults !!
----------------------------------------------------------------------------------------------------------------
If you use ViroProfiler for your analysis please cite:
* The ViroProfiler pipeline
Ru, Jinlong, et al. "ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis."
Gut Microbes 15.1 (2023): 2192522. https://doi.org/10.1080/19490976.2023.2192522
* The nf-core framework
Ewels, Philip A., et al. "The nf-core framework for community-curated bioinformatics pipelines."
Nature biotechnology 38.3 (2020): 276-278. https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/deng-lab/viroprofiler/blob/main/CITATIONS.md
----------------------------------------------------------------------------------------------------------------
[- ] process > VIROPROFILER:SETUP:DB_CHECKV -
[- ] process > VIROPROFILER:SETUP:DB_VIBRANT -
executor > local (3)
[- ] process > VIROPROFILER:SETUP:DB_CHECKV -
executor > local (3)
[- ] process > VIROPROFILER:SETUP:DB_CHECKV -
executor > local (3)
[- ] process > VIROPROFILER:SETUP:DB_CHECKV -
executor > local (3)
[- ] process > VIROPROFILER:SETUP:DB_CHECKV -
executor > local (3)
[- ] process > VIROPROFILER:SETUP:DB_CHECKV -
executor > local (3)
[- ] process > VIROPROFILER:SETUP:DB_CHECKV -
[84/c6b5c2] process > VIROPROFILER:SETUP:DB_VIBRANT [100%] 1 of 1, failed: 1 ✘
[ca/f0ce4e] process > VIROPROFILER:SETUP:DB_VIRSORTER2 [100%] 1 of 1, failed: 1 ✘
[- ] process > VIROPROFILER:SETUP:DB_DRAM -
[33/246c58] process > VIROPROFILER:SETUP:DB_IPHOP [100%] 1 of 1, failed: 1 ✘
[- ] process > VIROPROFILER:SETUP:DB_VREFSEQ -
Pulling Singularity image docker://denglab/viroprofiler-base:v0.2 [cache /media/bioinf/Data/singularity_cache/denglab-viroprofiler-base-v0.2.img]
Pulling Singularity image docker://denglab/viroprofiler-geneannot:v0.2 [cache /media/bioinf/Data/singularity_cache/denglab-viroprofiler-geneannot-v0.2.img]
Execution cancelled -- Finishing pending tasks before exit
-[ViroProfiler] Pipeline completed with errors-
ERROR ~ Error executing process > 'VIROPROFILER:SETUP:DB_VIBRANT'
Caused by:
Process `VIROPROFILER:SETUP:DB_VIBRANT` terminated with an error exit status (1)
Command executed:
if [ ! -d /media/bioinf/Data/viroprofiler/vibrant ]; then
mkdir -p /media/bioinf/Data/viroprofiler/vibrant
export VIBRANT_DATA_PATH="/opt/conda/share/vibrant-1.2.1/db"
download-db.sh /media/bioinf/Data/viroprofiler/vibrant
else
echo "VIBRANT database already exists"
fi
Command exit status:
1
Command output:
(empty)
Command error:
mkdir: cannot create directory ‘/media/bioinf/Data/viroprofiler/vibrant’: Read-only file system
Work dir:
/media/bioinf/Data/viroprofiler/work/84/c6b5c25b808e8aba045a107cb49ac9
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
-- Check '.nextflow.log' file for details
Same with sudo:
N E X T F L O W ~ version 23.04.3
Launching `https://github.com/deng-lab/viroprofiler` [angry_wing] DSL2 - revision: c2a1f1871b [main]
----------------------------------------------------------------------------------------------------------------
__
oooooo oooo o8o 88 88 .o88o. o8o oooo
`888. .8' `"' 88 ss 88 888 `" `"' `888
`888. .8' oooo oooo d8b .ooooo. 88__88 oooo d8b .ooooo. o888oo oooo 888 .ooooo. oooo d8b
`888. .8' `888 `888""8P d88' `88b || `888""8P d88' `88b 888 `888 888 d88' `88b `888""8P
`888.8' 888 888 888 888 _||_ 888 888 888 888 888 888 888ooo888 888
`888' 888 888 888 888 // || \\ 888 888 888 888 888 888 888 .o 888
`8' o888o d888b `Y8bod8P' // \\ d888b `Y8bod8P' o888o o888o o888o `Y8bod8P' d888b
ViroProfiler v0.2.4
----------------------------------------------------------------------------------------------------------------
Core Nextflow options
revision : main
runName : angry_wing
containerEngine: singularity
launchDir : /media/bioinf/Data/viroprofiler
workDir : /media/bioinf/Data/viroprofiler/work
projectDir : /home/bioinf/.nextflow/assets/deng-lab/viroprofiler
userName : root
profile : singularity
configFiles : /home/bioinf/.nextflow/assets/deng-lab/viroprofiler/nextflow.config
Input/output options
mode : setup
db : /media/bioinf/Data/viroprofiler
outdir : output
QC
contamref_idx : /home/bioinf/viroprofiler/contamination_refs/hg19/ref
Contig library parameters
assemblies : scaffolds
Others
use_iphop : true
use_dram : true
Max job request options
max_cpus : 1
max_memory : 8.GB
max_time : 12.h
!! Only displaying parameters that differ from the pipeline defaults !!
----------------------------------------------------------------------------------------------------------------
If you use ViroProfiler for your analysis please cite:
* The ViroProfiler pipeline
Ru, Jinlong, et al. "ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis."
Gut Microbes 15.1 (2023): 2192522. https://doi.org/10.1080/19490976.2023.2192522
* The nf-core framework
Ewels, Philip A., et al. "The nf-core framework for community-curated bioinformatics pipelines."
Nature biotechnology 38.3 (2020): 276-278. https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/deng-lab/viroprofiler/blob/main/CITATIONS.md
----------------------------------------------------------------------------------------------------------------
executor > local (2)
[- ] process > VIROPROFILER:SETUP:DB_CHECKV -
executor > local (3)
[- ] process > VIROPROFILER:SETUP:DB_CHECKV -
executor > local (3)
[- ] process > VIROPROFILER:SETUP:DB_CHECKV -
executor > local (3)
[- ] process > VIROPROFILER:SETUP:DB_CHECKV -
executor > local (3)
[- ] process > VIROPROFILER:SETUP:DB_CHECKV -
executor > local (3)
[- ] process > VIROPROFILER:SETUP:DB_CHECKV -
[e9/2a8e6a] process > VIROPROFILER:SETUP:DB_VIBRANT [100%] 1 of 1, failed: 1 ✘
[6b/e97a14] process > VIROPROFILER:SETUP:DB_VIRSORTER2 [100%] 1 of 1, failed: 1 ✘
[- ] process > VIROPROFILER:SETUP:DB_DRAM -
[24/3376dc] process > VIROPROFILER:SETUP:DB_IPHOP [100%] 1 of 1, failed: 1 ✘
[- ] process > VIROPROFILER:SETUP:DB_VREFSEQ -
Pulling Singularity image docker://denglab/viroprofiler-geneannot:v0.2 [cache /media/bioinf/Data/singularity_cache/denglab-viroprofiler-geneannot-v0.2.img]
Pulling Singularity image docker://denglab/viroprofiler-base:v0.2 [cache /media/bioinf/Data/singularity_cache/denglab-viroprofiler-base-v0.2.img]
Execution cancelled -- Finishing pending tasks before exit
-[ViroProfiler] Pipeline completed with errors-
ERROR ~ Error executing process > 'VIROPROFILER:SETUP:DB_VIBRANT'
Caused by:
Process `VIROPROFILER:SETUP:DB_VIBRANT` terminated with an error exit status (1)
Command executed:
if [ ! -d /media/bioinf/Data/viroprofiler/vibrant ]; then
mkdir -p /media/bioinf/Data/viroprofiler/vibrant
export VIBRANT_DATA_PATH="/opt/conda/share/vibrant-1.2.1/db"
download-db.sh /media/bioinf/Data/viroprofiler/vibrant
else
echo "VIBRANT database already exists"
fi
Command exit status:
1
Command output:
(empty)
Command error:
mkdir: cannot create directory ‘/media/bioinf/Data/viroprofiler/vibrant’: Read-only file system
Work dir:
/media/bioinf/Data/viroprofiler/work/e9/2a8e6a55c8e400100dbd97ec403619
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
-- Check '.nextflow.log' file for details
Description of the bug
Setup fails, complaining about inability to create a subfolder (
vibrant
) in the folder I supply with the--db
argument. Without custom--db
works fine, but I don't want the databases to be in my home folder.Command used and terminal output
Without
sudo
:Same with
sudo
:Relevant files
.nextflow.log
System information
Executed locally
Viroprofile v. 0.2.4
Containers: current example is with Singularity, but I've tried Docker with the same result.
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