ERROR ~ Error executing process > 'DENSE_WF:DENSE:TAXDUMP' #6
Description
Hi Authors, I encounter the following error message during installation.
(nextflow-25.3.0-el9) c1410:vlamba:~$ nextflow run i2bc/dense -profile singularity,test
N E X T F L O W ~ version 25.04.7
Launching https://github.com/i2bc/dense [astonishing_mestorf] DSL2 - revision: 18f5899 [master]
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Welcome to DENSE.
Core Nextflow options
revision : master
runName : astonishing_mestorf
containerEngine : singularity
container : [GENERA:docker://josuebarrera/genera, GENERA_FAST:docker://lopesi2bc/genera_fast, default:docker://lopesi2bc/denovogenes]
launchDir : /scrfs/storage/vlamba/home
workDir : /scrfs/storage/vlamba/home/work
projectDir : /home/vlamba/.nextflow/assets/i2bc/dense
userName : vlamba
profile : singularity,test
configFiles :
Input/output options
outdir : dense_results
gendir : /home/vlamba/.nextflow/assets/i2bc/dense/data/test/
Required input values
focal : Scer_chunk
Other important parameters
tree : /home/vlamba/.nextflow/assets/i2bc/dense/data/test/Saccharo_chunks.nwk
Institutional config options
config_profile_name : Test profile
config_profile_description: Minimal test dataset to check pipeline function
Max job request options
max_cpus : 1
max_memory : 2.GB
max_time : 6.h
TRG list options
genera_out : /home/vlamba/.nextflow/assets/i2bc/dense/data/test/559292_gene_ages.tsv
taxids : /home/vlamba/.nextflow/assets/i2bc/dense/data/test/taxids.tsv
!! Only displaying parameters that differ from the pipeline defaults !!
executor > local (2)
[bd/7770c0] DENSE_WF:DENSE:CHECK_INPUTS | 0 of 1
[- ] DENSE_WF:DENSE:EXTRACT_CDS -
[- ] DENSE_WF:DENSE:MRNA_TO_GENE -
[02/d71b35] DENSE_WF:DENSE:TAXDUMP | 0 of 1
[- ] DENSE_WF:DENSE:GENERA_FILTER -
[- ] DENSE_WF:DENSE:TRG_FNA -
[- ] DENSE_WF:DENSE:MULTIELONGATE_FOCAL_TRG -
[- ] DENSE_WF:DENSE:ELONGATE_CDS -
[- ] DENSE_WF:DENSE:BLAST -
[- ] DENSE_WF:DENSE:TRG_LIST_BEFORE_STRATEGY -
[- ] DENSE_WF:DENSE:BLAST_BEST_HITS -
[- ] DENSE_WF:DENSE:TREE_DISTANCES -
[- ] DENSE_WF:DENSE:TRG_TABLE -
[- ] DENSE_WF:DENSE:ORTHOLOGS:DIAMOND_BLAST -
[- ] DENSE_WF:DENSE:ORTHOLOGS:BEST_HITS -
[- ] DENSE_WF:DENSE:ORTHOLOGS:MRNA_TO_GENE -
[- ] DENSE_WF:DENSE:ORTHOLOGS:RECIPROCAL_BEST_HITS -
[- ] DENSE_WF:DENSE:CHECK_SYNTENY_INPUTS -
[- ] DENSE_WF:DENSE:CHECK_SYNTENY -
[- ] DENSE_WF:DENSE:SYNTENY_TO_TABLE -
Plus 2 more processes waiting for tasks…
ERROR ~ Error executing process > 'DENSE_WF:DENSE:TAXDUMP'
Caused by:
Process DENSE_WF:DENSE:TAXDUMP terminated with an error exit status (1)
Command executed:
If '--taxdump' is not provided,
if [ dummy == "dummy" ]
then
if [ ! -d /scrfs/storage/vlamba/home/work/taxdump ]
then
# Download it
# echo "Downloading ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.tar.gz"
# wget -N ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.tar.gz
# mkdir /scrfs/storage/vlamba/home/work/taxdump && tar zxf new_taxdump.tar.gz -C /scrfs/storage/vlamba/home/work/taxdump
echo "Downloading ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/new_taxdump_2023-03-01.zip"
echo "This will be only done once, and the taxdump directory will be kept for the next runs."
wget https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/new_taxdump_2023-03-01.zip
mkdir /scrfs/storage/vlamba/home/work/taxdump && unzip new_taxdump_2023-03-01.zip -d /scrfs/storage/vlamba/home/work/taxdump
fi
if [ ! -s /scrfs/storage/vlamba/home/work/taxdump/ncbi_lineages_2025-06-30.csv ]
then
echo "Downloading https://zenodo.org/records/15775019/files/ncbi_lineages_2025-06-30.csv?download=1"
wget https://zenodo.org/records/15775019/files/ncbi_lineages_2025-06-30.csv?download=1 -O /scrfs/storage/vlamba/home/work/taxdump/ncbi_lineages_2025-06-30.csv
fi
valid_taxdump="/scrfs/storage/vlamba/home/work/taxdump"
echo "The taxdump directory is ${valid_taxdump}. You can use '--taxdump ${valid_taxdump}'."
else
# Just keep taxdump as it is.
echo "The user provided a taxdump directory. Using it."
valid_taxdump=dummy
fi
executor > local (2)
[bd/7770c0] DENSE_WF:DENSE:CHECK_INPUTS | 0 of 1
[- ] DENSE_WF:DENSE:EXTRACT_CDS -
[- ] DENSE_WF:DENSE:MRNA_TO_GENE -
[02/d71b35] DENSE_WF:DENSE:TAXDUMP | 0 of 1 ✘
[- ] DENSE_WF:DENSE:GENERA_FILTER -
[- ] DENSE_WF:DENSE:TRG_FNA -
[- ] DENSE_WF:DENSE:MULTIELONGATE_FOCAL_TRG -
[- ] DENSE_WF:DENSE:ELONGATE_CDS -
[- ] DENSE_WF:DENSE:BLAST -
[- ] DENSE_WF:DENSE:TRG_LIST_BEFORE_STRATEGY -
[- ] DENSE_WF:DENSE:BLAST_BEST_HITS -
[- ] DENSE_WF:DENSE:TREE_DISTANCES -
[- ] DENSE_WF:DENSE:TRG_TABLE -
[- ] DENSE_WF:DENSE:ORTHOLOGS:DIAMOND_BLAST -
[- ] DENSE_WF:DENSE:ORTHOLOGS:BEST_HITS -
[- ] DENSE_WF:DENSE:ORTHOLOGS:MRNA_TO_GENE -
[- ] DENSE_WF:DENSE:ORTHOLOGS:RECIPROCAL_BEST_HITS -
[- ] DENSE_WF:DENSE:CHECK_SYNTENY_INPUTS -
[- ] DENSE_WF:DENSE:CHECK_SYNTENY -
[- ] DENSE_WF:DENSE:SYNTENY_TO_TABLE -
Plus 2 more processes waiting for tasks…
ERROR ~ Error executing process > 'DENSE_WF:DENSE:TAXDUMP'
Caused by:
Process DENSE_WF:DENSE:TAXDUMP terminated with an error exit status (1)
Command executed:
If '--taxdump' is not provided,
if [ dummy == "dummy" ]
then
if [ ! -d /scrfs/storage/vlamba/home/work/taxdump ]
then
# Download it
# echo "Downloading ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.tar.gz"
# wget -N ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.tar.gz
# mkdir /scrfs/storage/vlamba/home/work/taxdump && tar zxf new_taxdump.tar.gz -C /scrfs/storage/vlamba/home/work/taxdump
echo "Downloading ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/new_taxdump_2023-03-01.zip"
echo "This will be only done once, and the taxdump directory will be kept for the next runs."
wget https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/new_taxdump_2023-03-01.zip
mkdir /scrfs/storage/vlamba/home/work/taxdump && unzip new_taxdump_2023-03-01.zip -d /scrfs/storage/vlamba/home/work/taxdump
fi
if [ ! -s /scrfs/storage/vlamba/home/work/taxdump/ncbi_lineages_2025-06-30.csv ]
then
echo "Downloading https://zenodo.org/records/15775019/files/ncbi_lineages_2025-06-30.csv?download=1"
wget https://zenodo.org/records/15775019/files/ncbi_lineages_2025-06-30.csv?download=1 -O /scrfs/storage/vlamba/home/work/taxdump/ncbi_lineages_2025-06-30.csv
fi
valid_taxdump="/scrfs/storage/vlamba/home/work/taxdump"
echo "The taxdump directory is ${valid_taxdump}. You can use '--taxdump ${valid_taxdump}'."
else
# Just keep taxdump as it is.
echo "The user provided a taxdump directory. Using it."
valid_taxdump=dummy
fi
Command exit status:
1
Command output:
(empty)
Command error:
ERROR : No setuid installation found, for unprivileged installation use: ./mconfig --without-suid
Work dir:
/scrfs/storage/vlamba/home/work/02/d71b35991f589a763fb727ade007df
Container:
/home/vlamba/.nextflow/assets/i2bc/dense/containers/lopesi2bc-denovogenes.img
Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out
-- Check '.nextflow.log' file for details
I would really appreciate any suggestion/help to resolve this.
Thanks
V!