An error occurs when I execute the command "nextflow run deng-lab/viroprofiler -r main-profile singularity,test"
Command used and terminal output
(base) [root@develop viroprofiler]# nextflow run deng-lab/viroprofiler -r main -profile singularity,test
N E X T F L O W ~ version 23.04.1
Launching `https://github.com/deng-lab/viroprofiler` [ridiculous_wright] DSL2 - revision: c2a1f1871b [main]
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__
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ViroProfiler v0.2.4
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Core Nextflow options
revision : main
runName : ridiculous_wright
containerEngine : singularity
launchDir : /root/wanghang/viroprofiler/viropor/viroprofiler
workDir : /root/wanghang/viroprofiler/viropor/viroprofiler/work
projectDir : /root/.nextflow/assets/deng-lab/viroprofiler
userName : root
profile : singularity,test
configFiles : /root/.nextflow/assets/deng-lab/viroprofiler/nextflow.config
Input/output options
mode : all
input : https://raw.githubusercontent.com/deng-lab/viroprofiler/main/assets/samplesheet.csv
db : /root/wanghang/viroprofiler/viropor/viroprofiler
outdir : output
QC
contamref_idx : /root/viroprofiler/contamination_refs/hg19/ref
Contig library parameters
assemblies : scaffolds
Others
use_iphop : true
use_dram : true
Institutional config options
config_profile_name : Test profile
config_profile_description: Minimal test dataset to check pipeline function
Max job request options
max_cpus : 2
max_memory : 6.GB
max_time : 24.h
!! Only displaying parameters that differ from the pipeline defaults !!
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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
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[- ] process > VIROPROFILER:FASTQC -
[- ] process > VIROPROFILER:FASTP -
[- ] process > VIROPROFILER:FASTQC -
[- ] process > VIROPROFILER:FASTP -
[- ] process > VIROPROFILER:SPADES -
executor > local (2)
[63/8195fe] process > VIROPROFILER:FASTQC (HT04) [ 0%] 0 of 2
[- ] process > VIROPROFILER:FASTP [ 0%] 0 of 1
executor > local (4)
[63/8195fe] process > VIROPROFILER:FASTQC (HT04) [ 0%] 0 of 2
[97/67fff5] process > VIROPROFILER:FASTP (HT04) [ 0%] 0 of 2
executor > local (4)
[63/8195fe] process > VIROPROFILER:FASTQC (HT04) [ 0%] 0 of 2
[97/67fff5] process > VIROPROFILER:FASTP (HT04) [ 0%] 0 of 2
executor > local (4)
[63/8195fe] process > VIROPROFILER:FASTQC (HT04) [ 0%] 0 of 2
[97/67fff5] process > VIROPROFILER:FASTP (HT04) [ 0%] 0 of 2
executor > local (4)
[63/8195fe] process > VIROPROFILER:FASTQC (HT04) [ 0%] 0 of 2
[97/67fff5] process > VIROPROFILER:FASTP (HT04) [ 0%] 0 of 2
executor > local (6)
[29/7fe6d1] process > VIROPROFILER:FASTQC (UC20) [ 0%] 0 of 3
[74/30fe30] process > VIROPROFILER:FASTP (UC20) [ 0%] 0 of 3
executor > local (6)
[29/7fe6d1] process > VIROPROFILER:FASTQC (UC20) [ 0%] 0 of 3
[74/30fe30] process > VIROPROFILER:FASTP (UC20) [ 0%] 0 of 3
executor > local (6)
[63/8195fe] process > VIROPROFILER:FASTQC (HT04) [ 66%] 2 of 3
[74/30fe30] process > VIROPROFILER:FASTP (UC20) [ 0%] 0 of 3
executor > local (8)
[5f/4f4192] process > VIROPROFILER:FASTQC (UC21) [ 50%] 2 of 4
[57/dab04a] process > VIROPROFILER:FASTP (UC21) [ 0%] 0 of 4
executor > local (10)
[82/d3ae46] process > VIROPROFILER:FASTQC (UC24) [ 40%] 2 of 5
[7a/9b09f2] process > VIROPROFILER:FASTP (UC24) [ 0%] 0 of 5
executor > local (10)
[82/d3ae46] process > VIROPROFILER:FASTQC (UC24) [ 40%] 2 of 5
[84/f3c856] process > VIROPROFILER:FASTP (HT02) [ 20%] 1 of 5
[- ] process > VIROPROFILER:SPADES -
executor > local (10)
[29/7fe6d1] process > VIROPROFILER:FASTQC (UC20) [ 60%] 3 of 5
[84/f3c856] process > VIROPROFILER:FASTP (HT02) [ 20%] 1 of 5
[- ] process > VIROPROFILER:SPADES -
executor > local (10)
[5f/4f4192] process > VIROPROFILER:FASTQC (UC21) [ 80%] 4 of 5
[84/f3c856] process > VIROPROFILER:FASTP (HT02) [ 20%] 1 of 5
[- ] process > VIROPROFILER:SPADES -
executor > local (11)
[5f/4f4192] process > VIROPROFILER:FASTQC (UC21) [ 80%] 4 of 5
[84/f3c856] process > VIROPROFILER:FASTP (HT02) [ 20%] 1 of 5
[01/d0ee0f] process > VIROPROFILER:SPADES (HT02) [ 0%] 0 of 1
executor > local (11)
[5f/4f4192] process > VIROPROFILER:FASTQC (UC21) [ 80%] 4 of 5
[84/f3c856] process > VIROPROFILER:FASTP (HT02) [ 20%] 1 of 5
[01/d0ee0f] process > VIROPROFILER:SPADES (HT02) [ 0%] 0 of 1
executor > local (11)
[82/d3ae46] process > VIROPROFILER:FASTQC (UC24) [100%] 5 of 5 ✔
[84/f3c856] process > VIROPROFILER:FASTP (HT02) [ 20%] 1 of 5
[01/d0ee0f] process > VIROPROFILER:SPADES (HT02) [ 0%] 0 of 1
executor > local (12)
[82/d3ae46] process > VIROPROFILER:FASTQC (UC24) [100%] 5 of 5 ✔
[57/dab04a] process > VIROPROFILER:FASTP (UC21) [ 40%] 2 of 5
[68/8fca3d] process > VIROPROFILER:SPADES (UC21) [ 0%] 0 of 2
executor > local (13)
[82/d3ae46] process > VIROPROFILER:FASTQC (UC24) [100%] 5 of 5 ✔
[97/67fff5] process > VIROPROFILER:FASTP (HT04) [ 60%] 3 of 5
[96/8ea940] process > VIROPROFILER:SPADES (HT04) [ 0%] 0 of 3
executor > local (13)
[82/d3ae46] process > VIROPROFILER:FASTQC (UC24) [100%] 5 of 5 ✔
[97/67fff5] process > VIROPROFILER:FASTP (HT04) [ 60%] 3 of 5
[96/8ea940] process > VIROPROFILER:SPADES (HT04) [ 0%] 0 of 3
executor > local (15)
[82/d3ae46] process > VIROPROFILER:FASTQC (UC24) [100%] 5 of 5 ✔
[7a/9b09f2] process > VIROPROFILER:FASTP (UC24) [100%] 5 of 5 ✔
[b9/fad586] process > VIROPROFILER:SPADES (UC24) [ 0%] 0 of 5
executor > local (15)
[82/d3ae46] process > VIROPROFILER:FASTQC (UC24) [100%] 5 of 5 ✔
[7a/9b09f2] process > VIROPROFILER:FASTP (UC24) [100%] 5 of 5 ✔
[01/d0ee0f] process > VIROPROFILER:SPADES (HT02) [ 20%] 1 of 5
executor > local (15)
executor > local (15)
executor > local (16)
executor > local (17)
executor > local (19)
executor > local (19)
executor > local (21)
executor > local (21)
executor > local (22)
executor > local (22)
executor > local (22)
executor > local (22)
executor > local (32)
executor > local (33)
executor > local (34)
executor > local (34)
executor > local (34)
executor > local (37)
[82/d3ae46] process > VIROPROFILER:FASTQC (UC24) [100%] 5 of 5 ✔
[7a/9b09f2] process > VIROPROFILER:FASTP (UC24) [100%] 5 of 5 ✔
[97/17e074] process > VIROPROFILER:SPADES (UC20) [100%] 5 of 5 ✔
[c7/e36f95] process > VIROPROFILER:CONTIGLIB [100%] 1 of 1 ✔
[ce/17b9fa] process > VIROPROFILER:CHECKV [100%] 1 of 1 ✔
executor > local (37)
[82/d3ae46] process > VIROPROFILER:FASTQC (UC24) [100%] 5 of 5 ✔
[7a/9b09f2] process > VIROPROFILER:FASTP (UC24) [100%] 5 of 5 ✔
[97/17e074] process > VIROPROFILER:SPADES (UC20) [100%] 5 of 5 ✔
[c7/e36f95] process > VIROPROFILER:CONTIGLIB [100%] 1 of 1 ✔
[ce/17b9fa] process > VIROPROFILER:CHECKV [100%] 1 of 1 ✔
[64/46c405] process > VIROPROFILER:CONTIGLIB_CLUSTER [100%] 1 of 1 ✔
[9b/5486d6] process > VIROPROFILER:GENEPRED4CTG [100%] 1 of 1 ✔
[40/c60cf7] process > VIROPROFILER:NRPROT [100%] 1 of 1 ✔
[23/21ca21] process > VIROPROFILER:NRGENE [100%] 1 of 1 ✔
[00/d2bd9c] process > VIROPROFILER:CONTIGINDEX [100%] 1 of 1 ✔
[9b/381bbf] process > VIROPROFILER:MAPPING2CONTIGS2 (HT04) [100%] 5 of 5 ✔
[ad/6d2e49] process > VIROPROFILER:ABUNDANCE [100%] 1 of 1 ✔
[86/6145cc] process > VIROPROFILER:VIBRANT [100%] 1 of 1 ✔
[39/c98340] process > VIROPROFILER:DVF [100%] 1 of 1 ✔
[51/f7a743] process > VIROPROFILER:VIRCONTIGS_PRE [100%] 1 of 1 ✔
[aa/37b52b] process > VIROPROFILER:VIRSORTER2 [100%] 1 of 1 ✔
[83/b54606] process > VIROPROFILER:DRAMV [100%] 1 of 1, failed: 1 ✘
[20/bf03f7] process > VIROPROFILER:TAXONOMY_VCONTACT [ 0%] 0 of 1
[02/f44345] process > VIROPROFILER:TAXONOMY_MMSEQS [100%] 1 of 1 ✔
[- ] process > VIROPROFILER:TAXONOMY_MERGE -
[aa/fc290e] process > VIROPROFILER:VIRALHOST_IPHOP [ 0%] 0 of 1
[28/2c527b] process > VIROPROFILER:BACPHLIP [100%] 1 of 1 ✔
[- ] process > VIROPROFILER:RESULTS_TSE -
[- ] process > VIROPROFILER:CUSTOM_DUMPSOFTWAREVERSIONS -
[- ] process > VIROPROFILER:MULTIQC -
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'VIROPROFILER:DRAMV'
Caused by:
Process `VIROPROFILER:DRAMV` terminated with an error exit status (1)
Command executed:
# Due to limitation of container, DRAM database path is hardset to /opt/conda/db2
# So we need to create a soft link for the database path
ln -s /root/wanghang/viroprofiler/viropor/viroprofiler /opt/conda/db2
export DRAM_CONFIG_LOCATION=/root/wanghang/viroprofiler/viropor/viroprofiler/dram/CONFIG
DRAM-v.py annotate -i final-viral-combined-for-dramv.fa -v viral-affi-contigs-for-dramv.tab -o dramv-annotate --threads 1 --min_contig_size 3000
DRAM-v.py distill -i dramv-annotate/annotations.tsv -o dramv-distill
cat <<-END_VERSIONS > versions.yml
"VIROPROFILER:DRAMV":
DRAM: 1.3
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
ln: failed to create symbolic link '/opt/conda/db2': Read-only file system
Work dir:
/root/wanghang/viroprofiler/viropor/viroprofiler/work/83/b54606e343f92eaef4840413574f01
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
-- Check '.nextflow.log' file for details
Description of the bug
An error occurs when I execute the command "nextflow run deng-lab/viroprofiler -r main-profile singularity,test"
Command used and terminal output
Relevant files
No response
System information
No response