An error was encountered while running DADA2 in R (return code 1), inspect stdout and stderr to learn more

Zeina · April 11, 2026, 1:09pm

Hi everyone,

I encountered an issue while running DADA2 pipeline on 250 environmental samples. I submitted a job to a Slurm queue on a server.

qiime dada2 denoise-paired --i-demultiplexed-seqs data.qza --p-trunc-len-f 0 --p-trunc-len-r 240 --p-trim-left-f 18 --p-trim-left-r 20 --p-trunc-q 5 --p-n-threads 1 --o-table data-table.qza --o-representative-sequences data-rep-seqs.qza --o-denoising-stats data-denoisings-stats.qza

After 27 hours, I received the following error:

An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.

Debug info has been saved to /tmp/qiime2-q2cli-err-75hkokzg.log

Could you please assist?
Thank you!

lizgehret · April 15, 2026, 8:29am

Hey @Zeina,

Can you re-run your command with the --verbose flag enabled? And if possible, when re-submitting your job, include a .out file so that we can review the output once it re-runs; this will give us a better idea where the error is coming from.

Thanks!

Zeina · April 15, 2026, 9:08am

Thank you @lizgehret for you reply.
You can find below the .out output file.

---------------------------- /softs/contrib/modules ----------------------------
ams/2021.102
anaconda/2
anaconda/3
anvio/envs
aspera/3.9.7
bader/1.03
bioconda-tools/3
boost/1.70.0
boost/1.90.0
cast3m/2025
cgal/4.13.1
clFFT/2.12.2
cmake/3.22.1
code_saturne/5.1.6
code_saturne/6.0.0
CompEnvOpt/py312
crest/2.12
crest/3.0.2
cuda/11.4
demon/6.0.2
deMon/6.0.2
dftb+/25.1
ecp/bin
EEM/dos2unix/7.4.0
emacs/27.2
energy_scope/1.1.5
fftw/3.3.10
fftw/3.3.8
freefem++/4.7-1_petsc
freefem++/4.7-1_petsc-complex
gcc/11.2.0
gcc/15.2.0
git/2.19.2
gmp/6.1.2
grace/5.1
gromacs/2019.3
gromacs/2019.3-seq
gromacs/2021.1
GVenv/0.0.1
hdf5/1.12.3/intel/2019.4
hdf5-mpi/1.10.5
hysop/2.0.0-rc1
hysop/2024.11
hysop/2024.11_gpu
hysop/2024.11_nofftw
hysop/2024.11_nofftw_nompi
hysop/deps-gcc-11.2
hysop/devel-py3
hysop/devel-py310
hysop/devel-py311
hysop/devel-py312
idba/1.1.3-longseq
igmplot/2.6.9b
igmplot/3.08
iozone/3_508
iramuteq/0.7
irods/3.3.1
irods/4.2.11
irods/mcia
irods/mcia2
ISCDtoolbox/202204
ISCDtoolbox/202410
jags/4.3.0
jmol/14.30.0
julia/1.10.7
lammps/2020-10-29
lammps/2021-09-29
lapack/3.10.0/gcc/11.2.0
latep/ansys/v192
latep/ansys/v211
latep/ansys/v221
libxc/6.1.0
libxml2/2.10.4
llvm-clang/8.0.0
mcia-irods-password/0.1.3
mctdh84/16
molden/5.9
mpc/1.1.0
mpfr/4.0.2
multiwfn/3.6
multiwfn/3.8
nciplot/4.0
netcdf/4.9.2/intel/2019.4
obitools/4.2.0
octave/4.0.0/gcc/5.1.0
ogolem/reaxff
openfoam/10.0
openfoam/2106
openfoam/2212
openfoam/6.0
openjdk/21
openjdk/22.0.1
openmpi/4.1.2/gcc/11.2.0
openmpi/5.0.9/gcc/15.2.0
opentelemac/v7p2r1
opentelemac/v8p0r0
opentelemac/v8p2r0
orca/4.1.2
orca/5.0.4
orca/6.0.1
p4vasp/0.3.30
packmol/2009
paraview/4.4.0-mpi
paraview/5.6.1-mpi-test
paraview/5.8.0-mpi
paraview/5.8.0-mpi-gpu-egl
petsc/3.11.3/gcc/8.3.0
PETSc/3.11.3_superlu/gcc/8.3.0
phoronix-test-suite/10.8.4
phyloflash/3.4
plumed/2.5.3
plumed/2.6.0
plumed/2.6.1
pnetcdf/1.13.0/intel/2019.4
polyrate/17.C
pseudo_VASP/LDA
pseudo_VASP/PBE
pseudo_VASP/PW91
quantum_espresso/6.7.0/intel/2020.4
raspa/2.0.45
sage/9.2
scalapack/2.2.2/openmpi/5.0.9/gcc/15.2.0
scriptsGSV/0.0.1
slepc/3.11.1/gcc/8.3.0
stress-ng/0.19.05
suitesparse/5.11.0/gcc/11.2.0
swan/4131
sysbench/1.0.20
tomlab/8.9
travis/220729
turbomole/7.4.2
turbomole/7.5
umrtree/whisper/current
valgrind/3.15.0/gcc/9.1.0
vasp/5.4.4
vasp/5.4.4-VTST
vasp/6.3.2
VESTA/3.4.6
vmd/1.9.3
VTST-Tools/940
xcrysden/1.6.2
xtb/6.6.0
xtbiff/1.1
zoltan/3.901

-------------------------------- /softs/modules --------------------------------
avogadro/1.2.0 intel/oneapi/2021.4
cmake/3.14.4 intermol/0.1
cmake/3.5.0 MATLAB/R2023b
crystal/14 MATLAB/R2024a
crystal/17 megan/6
cst/2021 molpro/2015.1
cst/2022 molpro/2019.2
extrae/3.8.3/openmpi/1.10.7 molpro/2020.1
extrae/3.8.3/openmpi/3.1.4 molpro/2020.2
flexnet/current molpro/2022.3
freefem++/4.7-1 mrst/2023b
freetype/2.11.0 nbo/5
gaussian/g09-d01 nbo/6
gaussian/g16-b01 nbo/6.i8
gaussian/g16-c01 nbo/7
gaussview/5.0 nextflow/current
gaussview/6.0 openmpi/1.10.7/gcc/4.8.5
gcc/5.1.0 openmpi/2.1.0/intel/2019.4
gcc/7.3.0 openmpi/3.1.4/gcc/8.3.0
gcc/8.3.0 openmpi/4.1.4/gcc/11.2.0
gcc/9.1.0 ovito-basic/3.10.4
gdal/2.4.1 ovito-basic/3.5.4
gdal/3.12.1 paraver/4.9.2
geos/3.13.1 proj/9.6.0
gsl/2.5 pyrene-visu/current
intel/15.0 python/3
intel/2019.3 R/4.2.1
intel/2019.4 scilab/6.0.2
intel/2020.4 sqlite/3.49.1

conda environments:
                     /home/56/zeeb/miniconda3
                     /home/56/zeeb/miniconda3/envs/picrust1
                     /home/56/zeeb/miniconda3/envs/picrust2
base /softs/contrib/apps/anaconda/3
AmberTools23 /softs/contrib/apps/anaconda/3/envs/AmberTools23
R-4.4.3 /softs/contrib/apps/anaconda/3/envs/R-4.4.3
antismash-6.1.1 /softs/contrib/apps/anaconda/3/envs/antismash-6.1.1
antismash-7.0.0 /softs/contrib/apps/anaconda/3/envs/antismash-7.0.0
anvio-8 /softs/contrib/apps/anaconda/3/envs/anvio-8
bakta-1.7.0 /softs/contrib/apps/anaconda/3/envs/bakta-1.7.0
bbmap-39.01 /softs/contrib/apps/anaconda/3/envs/bbmap-39.01
beast-1.10.4 /softs/contrib/apps/anaconda/3/envs/beast-1.10.4
beast2-2.6.3 /softs/contrib/apps/anaconda/3/envs/beast2-2.6.3
bedtools-2.30.0 /softs/contrib/apps/anaconda/3/envs/bedtools-2.30.0
biopet-validatefastq-0.1.1 /softs/contrib/apps/anaconda/3/envs/biopet-validatefastq-0.1.1
biopython-1.76 /softs/contrib/apps/anaconda/3/envs/biopython-1.76
biopython-1.81 /softs/contrib/apps/anaconda/3/envs/biopython-1.81
blast-2.13.0 /softs/contrib/apps/anaconda/3/envs/blast-2.13.0
blast-qc-0.1 /softs/contrib/apps/anaconda/3/envs/blast-qc-0.1
bowtie2-2.5.1 /softs/contrib/apps/anaconda/3/envs/bowtie2-2.5.1
bwa-mem2-2.2.1 /softs/contrib/apps/anaconda/3/envs/bwa-mem2-2.2.1
c2mc /softs/contrib/apps/anaconda/3/envs/c2mc
cclib-1.7.2 /softs/contrib/apps/anaconda/3/envs/cclib-1.7.2
cd-hit-4.8.1 /softs/contrib/apps/anaconda/3/envs/cd-hit-4.8.1
checkm2-1.0.1 /softs/contrib/apps/anaconda/3/envs/checkm2-1.0.1
crest4-4.2.7 /softs/contrib/apps/anaconda/3/envs/crest4-4.2.7
curv /softs/contrib/apps/anaconda/3/envs/curv
cutadapt-4.2 /softs/contrib/apps/anaconda/3/envs/cutadapt-4.2
dbstep-1.1.0 /softs/contrib/apps/anaconda/3/envs/dbstep-1.1.0
dftbplus-25.1 /softs/contrib/apps/anaconda/3/envs/dftbplus-25.1
diamond-2.1.11 /softs/contrib/apps/anaconda/3/envs/diamond-2.1.11
eukrep-0.6.7 /softs/contrib/apps/anaconda/3/envs/eukrep-0.6.7
fast-virome-explorer-1.1.0.p2 /softs/contrib/apps/anaconda/3/envs/fast-virome-explorer-1.1.0.p2
fastp-0.23.4 /softs/contrib/apps/anaconda/3/envs/fastp-0.23.4
fastqc-0.11.9 /softs/contrib/apps/anaconda/3/envs/fastqc-0.11.9
figaro-1.1.2 /softs/contrib/apps/anaconda/3/envs/figaro-1.1.2
fluidfoam-0.2.4 /softs/contrib/apps/anaconda/3/envs/fluidfoam-0.2.4
gbseqextractor-0.0.4 /softs/contrib/apps/anaconda/3/envs/gbseqextractor-0.0.4
genemark_es-4.33 /softs/contrib/apps/anaconda/3/envs/genemark_es-4.33
genometools-genometools-1.6.2 /softs/contrib/apps/anaconda/3/envs/genometools-genometools-1.6.2
goodvibes-3.2 /softs/contrib/apps/anaconda/3/envs/goodvibes-3.2
gtdbtk-2.3.2 /softs/contrib/apps/anaconda/3/envs/gtdbtk-2.3.2
hmmer-3.3.2 /softs/contrib/apps/anaconda/3/envs/hmmer-3.3.2
idba-1.1.3 /softs/contrib/apps/anaconda/3/envs/idba-1.1.3
integron_finder-2.0.2 /softs/contrib/apps/anaconda/3/envs/integron_finder-2.0.2
intermol-0.1 /softs/contrib/apps/anaconda/3/envs/intermol-0.1
kma-1.3.22 /softs/contrib/apps/anaconda/3/envs/kma-1.3.22
kraken2-2.1.3 /softs/contrib/apps/anaconda/3/envs/kraken2-2.1.3
krona-2.8 /softs/contrib/apps/anaconda/3/envs/krona-2.8
lmp /softs/contrib/apps/anaconda/3/envs/lmp
mafft-7.525 /softs/contrib/apps/anaconda/3/envs/mafft-7.525
megahit-1.2.9 /softs/contrib/apps/anaconda/3/envs/megahit-1.2.9
metaeuk-7.bba0d80 /softs/contrib/apps/anaconda/3/envs/metaeuk-7.bba0d80
metaphlan-2.8.1 /softs/contrib/apps/anaconda/3/envs/metaphlan-2.8.1
metaphlan-3.0.13 /softs/contrib/apps/anaconda/3/envs/metaphlan-3.0.13
metaphlan-4.0.6 /softs/contrib/apps/anaconda/3/envs/metaphlan-4.0.6
metawrap-mg-1.3.0 /softs/contrib/apps/anaconda/3/envs/metawrap-mg-1.3.0
minimap2-2.24 /softs/contrib/apps/anaconda/3/envs/minimap2-2.24
mmseqs2-14.7e284 /softs/contrib/apps/anaconda/3/envs/mmseqs2-14.7e284
modeltest-ng-0.1.7 /softs/contrib/apps/anaconda/3/envs/modeltest-ng-0.1.7
mothur-1.47.0 /softs/contrib/apps/anaconda/3/envs/mothur-1.47.0
mrbayes-3.2.7 /softs/contrib/apps/anaconda/3/envs/mrbayes-3.2.7
mummer2circos-1.4.2 /softs/contrib/apps/anaconda/3/envs/mummer2circos-1.4.2
mummer4-4.0.0rc1 /softs/contrib/apps/anaconda/3/envs/mummer4-4.0.0rc1
muscle-5.1 /softs/contrib/apps/anaconda/3/envs/muscle-5.1
ncbi-amrfinderplus-3.12.8 /softs/contrib/apps/anaconda/3/envs/ncbi-amrfinderplus-3.12.8
openai-whisper-20231117 /softs/contrib/apps/anaconda/3/envs/openai-whisper-20231117
ovito-3.10.4 /softs/contrib/apps/anaconda/3/envs/ovito-3.10.4
phyloflash-3.4 /softs/contrib/apps/anaconda/3/envs/phyloflash-3.4
phylophlan-3.1.1 /softs/contrib/apps/anaconda/3/envs/phylophlan-3.1.1
picard-3.1.0 /softs/contrib/apps/anaconda/3/envs/picard-3.1.0
picrust2-2-2.0.3_b /softs/contrib/apps/anaconda/3/envs/picrust2-2-2.0.3_b
picrust2-2.4.2 /softs/contrib/apps/anaconda/3/envs/picrust2-2.4.2
picrust2-2.5.0 /softs/contrib/apps/anaconda/3/envs/picrust2-2.5.0
picrust2-2.5.3 /softs/contrib/apps/anaconda/3/envs/picrust2-2.5.3
pipits-2.8 /softs/contrib/apps/anaconda/3/envs/pipits-2.8
pipits-3.0 /softs/contrib/apps/anaconda/3/envs/pipits-3.0
pmg /softs/contrib/apps/anaconda/3/envs/pmg
prodigal-2.6.3 /softs/contrib/apps/anaconda/3/envs/prodigal-2.6.3
prokka-1.14.6 /softs/contrib/apps/anaconda/3/envs/prokka-1.14.6
pypdf-5.0.1 /softs/contrib/apps/anaconda/3/envs/pypdf-5.0.1
qiime2-2019.10 /softs/contrib/apps/anaconda/3/envs/qiime2-2019.10
qiime2-2023.7 /softs/contrib/apps/anaconda/3/envs/qiime2-2023.7
qiime2-amplicon-2024.5 * /softs/contrib/apps/anaconda/3/envs/qiime2-amplicon-2024.5
qiime2-amplicon-2025.4 /softs/contrib/apps/anaconda/3/envs/qiime2-amplicon-2025.4
quast-5.2.0 /softs/contrib/apps/anaconda/3/envs/quast-5.2.0
r-virfinder-1.1 /softs/contrib/apps/anaconda/3/envs/r-virfinder-1.1
ragtag-2.1.0 /softs/contrib/apps/anaconda/3/envs/ragtag-2.1.0
raxml-ng-1.2.1 /softs/contrib/apps/anaconda/3/envs/raxml-ng-1.2.1
rnaquast-2.2.3 /softs/contrib/apps/anaconda/3/envs/rnaquast-2.2.3
samtools-1.17 /softs/contrib/apps/anaconda/3/envs/samtools-1.17
sortmerna-4.3.6 /softs/contrib/apps/anaconda/3/envs/sortmerna-4.3.6
sourcetracker-2.0.1 /softs/contrib/apps/anaconda/3/envs/sourcetracker-2.0.1
spades-3.15.5 /softs/contrib/apps/anaconda/3/envs/spades-3.15.5
squeezemeta-1.7.2 /softs/contrib/apps/anaconda/3/envs/squeezemeta-1.7.2
sra-tools-3.0.7 /softs/contrib/apps/anaconda/3/envs/sra-tools-3.0.7
stan-r-tools-2.36.0 /softs/contrib/apps/anaconda/3/envs/stan-r-tools-2.36.0
trim-galore-0.6.6 /softs/contrib/apps/anaconda/3/envs/trim-galore-0.6.6
trimmomatic-0.39 /softs/contrib/apps/anaconda/3/envs/trimmomatic-0.39
virsorter-2.2.3 /softs/contrib/apps/anaconda/3/envs/virsorter-2.2.3
vsearch-2.22.1 /softs/contrib/apps/anaconda/3/envs/vsearch-2.22.1

Usage: qiime [OPTIONS] COMMAND [ARGS]...

QIIME 2 command-line interface (q2cli)

To get help with QIIME 2, visit https://qiime2.org.

To enable tab completion in Bash, run the following command or add it to
your .bashrc/.bash_profile:
  source tab-qiime
To enable tab completion in ZSH, run the following commands or add them to
your .zshrc:
  autoload -Uz compinit && compinit
  autoload bashcompinit && bashcompinit
  source tab-qiime
Options:
--version Show the version and exit.
--help Show this message and exit.

Commands:
info Display information about current deployment.
tools Tools for working with QIIME 2 files.
dev Utilities for developers and advanced users.
alignment Plugin for generating and manipulating alignments.
composition Plugin for compositional data analysis.
cutadapt Plugin for removing adapter sequences, primers, and
other unwanted sequence from sequence data.
dada2 Plugin for sequence quality control with DADA2.
deblur Plugin for sequence quality control with Deblur.
demux Plugin for demultiplexing & viewing sequence quality.
diversity Plugin for exploring community diversity.
diversity-lib Plugin for computing community diversity.
emperor Plugin for ordination plotting with Emperor.
feature-classifier Plugin for taxonomic classification.
feature-table Plugin for working with sample by feature tables.
fondue Plugin for fetching sequences and metadata.
fragment-insertion Plugin for extending phylogenies.
krona Plugin for creating Krona plots.
longitudinal Plugin for paired sample and time series analyses.
metadata Plugin for working with Metadata.
phylogeny Plugin for generating and manipulating phylogenies.
quality-control Plugin for quality control of feature and sequence data.
quality-filter Plugin for PHRED-based filtering and trimming.
repeat-rarefy Repeat rarefy method.
rescript Pipeline for reference sequence annotation and curation.
sample-classifier Plugin for machine learning prediction of sample
metadata.
taxa Plugin for working with feature taxonomy annotations.
vsearch Plugin for clustering and dereplicating with vsearch.
dos2unix: converting file manifest.txt to Unix format...
Plugin error from dada2:

An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.

Debug info has been saved to /tmp/qiime2-q2cli-err-75hkokzg.log

lizgehret · April 15, 2026, 9:11am

Hey @Zeina,

I'll need the .out file after you re-run your command with the --verbose flag enabled. This will provide more details within the subprocess call to R, which will allow us to see where exactly the error is coming from.

Cheers

Zeina · April 17, 2026, 10:27am

Hi @ lizgehret,

I ran the command with the --verbose option, and I got the output below.

Thank you


---------------------------- /softs/contrib/modules ----------------------------
ams/2021.102
anaconda/2
anaconda/3
anvio/envs
aspera/3.9.7
bader/1.03
bioconda-tools/3
boost/1.70.0
boost/1.90.0
cast3m/2025
cgal/4.13.1
clFFT/2.12.2
cmake/3.22.1
code_saturne/5.1.6
code_saturne/6.0.0
CompEnvOpt/py312
crest/2.12
crest/3.0.2
cuda/11.4
demon/6.0.2
deMon/6.0.2
dftb+/25.1
ecp/bin
EEM/dos2unix/7.4.0
emacs/27.2
energy_scope/1.1.5
fftw/3.3.10
fftw/3.3.8
freefem++/4.7-1_petsc
freefem++/4.7-1_petsc-complex
gcc/11.2.0
gcc/15.2.0
git/2.19.2
gmp/6.1.2
grace/5.1
gromacs/2019.3
gromacs/2019.3-seq
gromacs/2021.1
GVenv/0.0.1
hdf5/1.12.3/intel/2019.4
hdf5-mpi/1.10.5
hysop/2.0.0-rc1
hysop/2024.11
hysop/2024.11_gpu
hysop/2024.11_nofftw
hysop/2024.11_nofftw_nompi
hysop/deps-gcc-11.2
hysop/devel-py3
hysop/devel-py310
hysop/devel-py311
hysop/devel-py312
idba/1.1.3-longseq
igmplot/2.6.9b
igmplot/3.08
iozone/3_508
iramuteq/0.7
irods/3.3.1
irods/4.2.11
irods/mcia
irods/mcia2
ISCDtoolbox/202204
ISCDtoolbox/202410
jags/4.3.0
jmol/14.30.0
julia/1.10.7
lammps/2020-10-29
lammps/2021-09-29
lapack/3.10.0/gcc/11.2.0
latep/ansys/v192
latep/ansys/v211
latep/ansys/v221
libxc/6.1.0
libxml2/2.10.4
llvm-clang/8.0.0
mcia-irods-password/0.1.3
mctdh84/16
molden/5.9
mpc/1.1.0
mpfr/4.0.2
multiwfn/3.6
multiwfn/3.8
nciplot/4.0
netcdf/4.9.2/intel/2019.4
obitools/4.2.0
octave/4.0.0/gcc/5.1.0
ogolem/reaxff
openfoam/10.0
openfoam/2106
openfoam/2212
openfoam/6.0
openjdk/21
openjdk/22.0.1
openmpi/4.1.2/gcc/11.2.0
openmpi/5.0.9/gcc/15.2.0
opentelemac/v7p2r1
opentelemac/v8p0r0
opentelemac/v8p2r0
orca/4.1.2
orca/5.0.4
orca/6.0.1
p4vasp/0.3.30
packmol/2009
paraview/4.4.0-mpi
paraview/5.6.1-mpi-test
paraview/5.8.0-mpi
paraview/5.8.0-mpi-gpu-egl
petsc/3.11.3/gcc/8.3.0
PETSc/3.11.3_superlu/gcc/8.3.0
phoronix-test-suite/10.8.4
phyloflash/3.4
plumed/2.5.3
plumed/2.6.0
plumed/2.6.1
pnetcdf/1.13.0/intel/2019.4
polyrate/17.C
pseudo_VASP/LDA
pseudo_VASP/PBE
pseudo_VASP/PW91
quantum_espresso/6.7.0/intel/2020.4
raspa/2.0.45
sage/9.2
scalapack/2.2.2/openmpi/5.0.9/gcc/15.2.0
scriptsGSV/0.0.1
slepc/3.11.1/gcc/8.3.0
stress-ng/0.19.05
suitesparse/5.11.0/gcc/11.2.0
swan/4131
sysbench/1.0.20
tomlab/8.9
travis/220729
turbomole/7.4.2
turbomole/7.5
umrtree/whisper/current
valgrind/3.15.0/gcc/9.1.0
vasp/5.4.4
vasp/5.4.4-VTST
vasp/6.3.2
VESTA/3.4.6
vmd/1.9.3
VTST-Tools/940
xcrysden/1.6.2
xtb/6.6.0
xtbiff/1.1
zoltan/3.901

-------------------------------- /softs/modules --------------------------------
avogadro/1.2.0              intel/oneapi/2021.4
cmake/3.14.4                intermol/0.1
cmake/3.5.0                 MATLAB/R2023b
crystal/14                  MATLAB/R2024a
crystal/17                  megan/6
cst/2021                    molpro/2015.1
cst/2022                    molpro/2019.2
extrae/3.8.3/openmpi/1.10.7 molpro/2020.1
extrae/3.8.3/openmpi/3.1.4  molpro/2020.2
flexnet/current             molpro/2022.3
freefem++/4.7-1             mrst/2023b
freetype/2.11.0             nbo/5
gaussian/g09-d01            nbo/6
gaussian/g16-b01            nbo/6.i8
gaussian/g16-c01            nbo/7
gaussview/5.0               nextflow/current
gaussview/6.0               openmpi/1.10.7/gcc/4.8.5
gcc/5.1.0                   openmpi/2.1.0/intel/2019.4
gcc/7.3.0                   openmpi/3.1.4/gcc/8.3.0
gcc/8.3.0                   openmpi/4.1.4/gcc/11.2.0
gcc/9.1.0                   ovito-basic/3.10.4
gdal/2.4.1                  ovito-basic/3.5.4
gdal/3.12.1                 paraver/4.9.2
geos/3.13.1                 proj/9.6.0
gsl/2.5                     pyrene-visu/current
intel/15.0                  python/3
intel/2019.3                R/4.2.1
intel/2019.4                scilab/6.0.2
intel/2020.4                sqlite/3.49.1
# conda environments:
#
                         /home/56/zee/miniconda3
                         /home/56/zee/miniconda3/envs/picrust1
                         /home/56/zee/miniconda3/envs/picrust2
base                     /softs/contrib/apps/anaconda/3
AmberTools23             /softs/contrib/apps/anaconda/3/envs/AmberTools23
R-4.4.3                  /softs/contrib/apps/anaconda/3/envs/R-4.4.3
antismash-6.1.1          /softs/contrib/apps/anaconda/3/envs/antismash-6.1.1
antismash-7.0.0          /softs/contrib/apps/anaconda/3/envs/antismash-7.0.0
anvio-8                  /softs/contrib/apps/anaconda/3/envs/anvio-8
bakta-1.7.0              /softs/contrib/apps/anaconda/3/envs/bakta-1.7.0
bbmap-39.01              /softs/contrib/apps/anaconda/3/envs/bbmap-39.01
beast-1.10.4             /softs/contrib/apps/anaconda/3/envs/beast-1.10.4
beast2-2.6.3             /softs/contrib/apps/anaconda/3/envs/beast2-2.6.3
bedtools-2.30.0          /softs/contrib/apps/anaconda/3/envs/bedtools-2.30.0
biopet-validatefastq-0.1.1     /softs/contrib/apps/anaconda/3/envs/biopet-validatefastq-0.1.1
biopython-1.76           /softs/contrib/apps/anaconda/3/envs/biopython-1.76
biopython-1.81           /softs/contrib/apps/anaconda/3/envs/biopython-1.81
blast-2.13.0             /softs/contrib/apps/anaconda/3/envs/blast-2.13.0
blast-qc-0.1             /softs/contrib/apps/anaconda/3/envs/blast-qc-0.1
bowtie2-2.5.1            /softs/contrib/apps/anaconda/3/envs/bowtie2-2.5.1
bwa-mem2-2.2.1           /softs/contrib/apps/anaconda/3/envs/bwa-mem2-2.2.1
c2mc                     /softs/contrib/apps/anaconda/3/envs/c2mc
cclib-1.7.2              /softs/contrib/apps/anaconda/3/envs/cclib-1.7.2
cd-hit-4.8.1             /softs/contrib/apps/anaconda/3/envs/cd-hit-4.8.1
checkm2-1.0.1            /softs/contrib/apps/anaconda/3/envs/checkm2-1.0.1
crest4-4.2.7             /softs/contrib/apps/anaconda/3/envs/crest4-4.2.7
curv                     /softs/contrib/apps/anaconda/3/envs/curv
cutadapt-4.2             /softs/contrib/apps/anaconda/3/envs/cutadapt-4.2
dbstep-1.1.0             /softs/contrib/apps/anaconda/3/envs/dbstep-1.1.0
dftbplus-25.1            /softs/contrib/apps/anaconda/3/envs/dftbplus-25.1
diamond-2.1.11           /softs/contrib/apps/anaconda/3/envs/diamond-2.1.11
eukrep-0.6.7             /softs/contrib/apps/anaconda/3/envs/eukrep-0.6.7
fast-virome-explorer-1.1.0.p2     /softs/contrib/apps/anaconda/3/envs/fast-virome-explorer-1.1.0.p2
fastp-0.23.4             /softs/contrib/apps/anaconda/3/envs/fastp-0.23.4
fastqc-0.11.9            /softs/contrib/apps/anaconda/3/envs/fastqc-0.11.9
figaro-1.1.2             /softs/contrib/apps/anaconda/3/envs/figaro-1.1.2
fluidfoam-0.2.4          /softs/contrib/apps/anaconda/3/envs/fluidfoam-0.2.4
gbseqextractor-0.0.4     /softs/contrib/apps/anaconda/3/envs/gbseqextractor-0.0.4
genemark_es-4.33         /softs/contrib/apps/anaconda/3/envs/genemark_es-4.33
genometools-genometools-1.6.2     /softs/contrib/apps/anaconda/3/envs/genometools-genometools-1.6.2
goodvibes-3.2            /softs/contrib/apps/anaconda/3/envs/goodvibes-3.2
gtdbtk-2.3.2             /softs/contrib/apps/anaconda/3/envs/gtdbtk-2.3.2
hmmer-3.3.2              /softs/contrib/apps/anaconda/3/envs/hmmer-3.3.2
idba-1.1.3               /softs/contrib/apps/anaconda/3/envs/idba-1.1.3
integron_finder-2.0.2     /softs/contrib/apps/anaconda/3/envs/integron_finder-2.0.2
intermol-0.1             /softs/contrib/apps/anaconda/3/envs/intermol-0.1
kma-1.3.22               /softs/contrib/apps/anaconda/3/envs/kma-1.3.22
kraken2-2.1.3            /softs/contrib/apps/anaconda/3/envs/kraken2-2.1.3
krona-2.8                /softs/contrib/apps/anaconda/3/envs/krona-2.8
lmp                      /softs/contrib/apps/anaconda/3/envs/lmp
mafft-7.525              /softs/contrib/apps/anaconda/3/envs/mafft-7.525
megahit-1.2.9            /softs/contrib/apps/anaconda/3/envs/megahit-1.2.9
metaeuk-7.bba0d80        /softs/contrib/apps/anaconda/3/envs/metaeuk-7.bba0d80
metaphlan-2.8.1          /softs/contrib/apps/anaconda/3/envs/metaphlan-2.8.1
metaphlan-3.0.13         /softs/contrib/apps/anaconda/3/envs/metaphlan-3.0.13
metaphlan-4.0.6          /softs/contrib/apps/anaconda/3/envs/metaphlan-4.0.6
metawrap-mg-1.3.0        /softs/contrib/apps/anaconda/3/envs/metawrap-mg-1.3.0
minimap2-2.24            /softs/contrib/apps/anaconda/3/envs/minimap2-2.24
mmseqs2-14.7e284         /softs/contrib/apps/anaconda/3/envs/mmseqs2-14.7e284
modeltest-ng-0.1.7       /softs/contrib/apps/anaconda/3/envs/modeltest-ng-0.1.7
mothur-1.47.0            /softs/contrib/apps/anaconda/3/envs/mothur-1.47.0
mrbayes-3.2.7            /softs/contrib/apps/anaconda/3/envs/mrbayes-3.2.7
mummer2circos-1.4.2      /softs/contrib/apps/anaconda/3/envs/mummer2circos-1.4.2
mummer4-4.0.0rc1         /softs/contrib/apps/anaconda/3/envs/mummer4-4.0.0rc1
muscle-5.1               /softs/contrib/apps/anaconda/3/envs/muscle-5.1
ncbi-amrfinderplus-3.12.8     /softs/contrib/apps/anaconda/3/envs/ncbi-amrfinderplus-3.12.8
openai-whisper-20231117     /softs/contrib/apps/anaconda/3/envs/openai-whisper-20231117
ovito-3.10.4             /softs/contrib/apps/anaconda/3/envs/ovito-3.10.4
phyloflash-3.4           /softs/contrib/apps/anaconda/3/envs/phyloflash-3.4
phylophlan-3.1.1         /softs/contrib/apps/anaconda/3/envs/phylophlan-3.1.1
picard-3.1.0             /softs/contrib/apps/anaconda/3/envs/picard-3.1.0
picrust2-2-2.0.3_b       /softs/contrib/apps/anaconda/3/envs/picrust2-2-2.0.3_b
picrust2-2.4.2           /softs/contrib/apps/anaconda/3/envs/picrust2-2.4.2
picrust2-2.5.0           /softs/contrib/apps/anaconda/3/envs/picrust2-2.5.0
picrust2-2.5.3           /softs/contrib/apps/anaconda/3/envs/picrust2-2.5.3
pipits-2.8               /softs/contrib/apps/anaconda/3/envs/pipits-2.8
pipits-3.0               /softs/contrib/apps/anaconda/3/envs/pipits-3.0
pmg                      /softs/contrib/apps/anaconda/3/envs/pmg
prodigal-2.6.3           /softs/contrib/apps/anaconda/3/envs/prodigal-2.6.3
prokka-1.14.6            /softs/contrib/apps/anaconda/3/envs/prokka-1.14.6
pypdf-5.0.1              /softs/contrib/apps/anaconda/3/envs/pypdf-5.0.1
qiime2-2019.10           /softs/contrib/apps/anaconda/3/envs/qiime2-2019.10
qiime2-2023.7            /softs/contrib/apps/anaconda/3/envs/qiime2-2023.7
qiime2-amplicon-2024.5  *  /softs/contrib/apps/anaconda/3/envs/qiime2-amplicon-2024.5
qiime2-amplicon-2025.4     /softs/contrib/apps/anaconda/3/envs/qiime2-amplicon-2025.4
quast-5.2.0              /softs/contrib/apps/anaconda/3/envs/quast-5.2.0
r-virfinder-1.1          /softs/contrib/apps/anaconda/3/envs/r-virfinder-1.1
ragtag-2.1.0             /softs/contrib/apps/anaconda/3/envs/ragtag-2.1.0
raxml-ng-1.2.1           /softs/contrib/apps/anaconda/3/envs/raxml-ng-1.2.1
rnaquast-2.2.3           /softs/contrib/apps/anaconda/3/envs/rnaquast-2.2.3
samtools-1.17            /softs/contrib/apps/anaconda/3/envs/samtools-1.17
sortmerna-4.3.6          /softs/contrib/apps/anaconda/3/envs/sortmerna-4.3.6
sourcetracker-2.0.1      /softs/contrib/apps/anaconda/3/envs/sourcetracker-2.0.1
spades-3.15.5            /softs/contrib/apps/anaconda/3/envs/spades-3.15.5
squeezemeta-1.7.2        /softs/contrib/apps/anaconda/3/envs/squeezemeta-1.7.2
sra-tools-3.0.7          /softs/contrib/apps/anaconda/3/envs/sra-tools-3.0.7
stan-r-tools-2.36.0      /softs/contrib/apps/anaconda/3/envs/stan-r-tools-2.36.0
trim-galore-0.6.6        /softs/contrib/apps/anaconda/3/envs/trim-galore-0.6.6
trimmomatic-0.39         /softs/contrib/apps/anaconda/3/envs/trimmomatic-0.39
virsorter-2.2.3          /softs/contrib/apps/anaconda/3/envs/virsorter-2.2.3
vsearch-2.22.1           /softs/contrib/apps/anaconda/3/envs/vsearch-2.22.1

Usage: qiime [OPTIONS] COMMAND [ARGS]...

  QIIME 2 command-line interface (q2cli)
  --------------------------------------

  To get help with QIIME 2, visit https://qiime2.org.

  To enable tab completion in Bash, run the following command or add it to
  your .bashrc/.bash_profile:

      source tab-qiime

  To enable tab completion in ZSH, run the following commands or add them to
  your .zshrc:

      autoload -Uz compinit && compinit
      autoload bashcompinit && bashcompinit
      source tab-qiime

Options:
  --version   Show the version and exit.
  --help      Show this message and exit.

Commands:
  info                Display information about current deployment.
  tools               Tools for working with QIIME 2 files.
  dev                 Utilities for developers and advanced users.
  alignment           Plugin for generating and manipulating alignments.
  composition         Plugin for compositional data analysis.
  cutadapt            Plugin for removing adapter sequences, primers, and
                      other unwanted sequence from sequence data.
  dada2               Plugin for sequence quality control with DADA2.
  deblur              Plugin for sequence quality control with Deblur.
  demux               Plugin for demultiplexing & viewing sequence quality.
  diversity           Plugin for exploring community diversity.
  diversity-lib       Plugin for computing community diversity.
  emperor             Plugin for ordination plotting with Emperor.
  feature-classifier  Plugin for taxonomic classification.
  feature-table       Plugin for working with sample by feature tables.
  fondue              Plugin for fetching sequences and metadata.
  fragment-insertion  Plugin for extending phylogenies.
  krona               Plugin for creating Krona plots.
  longitudinal        Plugin for paired sample and time series analyses.
  metadata            Plugin for working with Metadata.
  phylogeny           Plugin for generating and manipulating phylogenies.
  quality-control     Plugin for quality control of feature and sequence data.
  quality-filter      Plugin for PHRED-based filtering and trimming.
  repeat-rarefy       Repeat rarefy method.
  rescript            Pipeline for reference sequence annotation and curation.
  sample-classifier   Plugin for machine learning prediction of sample
                      metadata.
  taxa                Plugin for working with feature taxonomy annotations.
  vsearch             Plugin for clustering and dereplicating with vsearch.
dos2unix: converting file manifest.txt to Unix format...
R version 4.3.3 (2024-02-29) 
Loading required package: Rcpp
DADA2: 1.30.0 / Rcpp: 1.0.12 / RcppParallel: 5.1.6 
2) Filtering ...........................................................................................................................................................................................................................................................
3) Learning Error Rates
247873769 total bases in 1042070 reads from 13 samples will be used for learning the error rates.
229255400 total bases in 1042070 reads from 13 samples will be used for learning the error rates.
3) Denoise samples ..............................................................................................................................................Error in derepFastq(filtsR[[j]]) : Not all provided files exist.
2: stop("Not all provided files exist.")
1: derepFastq(filtsR[[j]])
Traceback (most recent call last):
  File "/softs/contrib/apps/anaconda/3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_dada2/_denoise.py", line 350, in denoise_paired
    run_commands([cmd])
  File "/softs/contrib/apps/anaconda/3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_dada2/_denoise.py", line 37, in run_commands
    subprocess.run(cmd, check=True)
  File "/softs/contrib/apps/anaconda/3/envs/qiime2-amplicon-2024.5/lib/python3.9/subprocess.py", line 528, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run_dada.R', '--input_directory', '/tmp/tmpw_k3h3wl/forward', '--input_directory_reverse', '/tmp/tmpw_k3h3wl/reverse', '--output_path', '/tmp/tmpw_k3h3wl/output.tsv.biom', '--output_track', '/tmp/tmpw_k3h3wl/track.tsv', '--filtered_directory', '/tmp/tmpw_k3h3wl/filt_f', '--filtered_directory_reverse', '/tmp/tmpw_k3h3wl/filt_r', '--truncation_length', '0', '--truncation_length_reverse', '240', '--trim_left', '18', '--trim_left_reverse', '20', '--max_expected_errors', '2.0', '--max_expected_errors_reverse', '2.0', '--truncation_quality_score', '5', '--min_overlap', '12', '--pooling_method', 'independent', '--chimera_method', 'consensus', '--min_parental_fold', '1.0', '--allow_one_off', 'False', '--num_threads', '1', '--learn_min_reads', '1000000']' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/softs/contrib/apps/anaconda/3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
    outputs = self._callable_executor_(
  File "/softs/contrib/apps/anaconda/3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 576, in _callable_executor_
    output_views = self._callable(**view_args)
  File "/softs/contrib/apps/anaconda/3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_dada2/_denoise.py", line 363, in denoise_paired
    raise Exception("An error was encountered while running DADA2"
Exception: An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/softs/contrib/apps/anaconda/3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/commands.py", line 520, in __call__
    results = self._execute_action(
  File "/softs/contrib/apps/anaconda/3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/commands.py", line 581, in _execute_action
    results = action(**arguments)
  File "<decorator-gen-49>", line 2, in denoise_paired
  File "/softs/contrib/apps/anaconda/3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 356, in bound_callable
    return results
  File "/softs/contrib/apps/anaconda/3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/context.py", line 195, in __exit__
    self._scope.destroy()
  File "/softs/contrib/apps/anaconda/3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/context.py", line 269, in destroy
    ctx.cache.garbage_collection()
  File "/softs/contrib/apps/anaconda/3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/core/cache.py", line 740, in garbage_collection
    for key in self.get_keys():
  File "/softs/contrib/apps/anaconda/3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/core/cache.py", line 1250, in get_keys
    return set(os.listdir(self.keys))
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/qiime2/zee/keys'

Plugin error from dada2:

  [Errno 2] No such file or directory: '/tmp/qiime2/zee/keys'

See above for debug info.
Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.

Command: run_dada.R --input_directory /tmp/tmpw_k3h3wl/forward --input_directory_reverse /tmp/tmpw_k3h3wl/reverse --output_path /tmp/tmpw_k3h3wl/output.tsv.biom --output_track /tmp/tmpw_k3h3wl/track.tsv --filtered_directory /tmp/tmpw_k3h3wl/filt_f --filtered_directory_reverse /tmp/tmpw_k3h3wl/filt_r --truncation_length 0 --truncation_length_reverse 240 --trim_left 18 --trim_left_reverse 20 --max_expected_errors 2.0 --max_expected_errors_reverse 2.0 --truncation_quality_score 5 --min_overlap 12 --pooling_method independent --chimera_method consensus --min_parental_fold 1.0 --allow_one_off False --num_threads 1 --learn_min_reads 1000000

cherman2 · April 21, 2026, 2:48pm

Hi @Zeina,
This is a weird error! Scrolling through your output it looks like this is the reason DADA2 failed.

I am not quite sure why this would happen. Have you done any filtering before DADA2?

Sorry, I dont have an exact answer right now, but I am sure we can figure it out

Zeina · April 21, 2026, 3:22pm

Hi @cherman2,

No, I did not. I only have the forward and reverse reads generated by the step below, and they look good.


qiime demux summarize --i-data data.qza --o-visualization data.qzv

Zeina

cherman2 · April 21, 2026, 9:19pm

hey @Zeina,
Would you mind sharing your demux.qza so I can debug this? Feel free to DM me the file if you don't want to share your data publicly!
Thanks!

Zeina · April 22, 2026, 10:51am

Hi @cherman2 , how can I DM you to share the requested file ?

cherman2 · April 28, 2026, 6:57pm

Hi @Zeina,
Sorry for my slow reply! I was able to successfully run dada2 on your data.

This unfortunately suggests that the file(s) that are not being found are probably an issue with your HPC's file handling.

Have you brought this up with your HPC team? If so, do they have any thoughts?

Zeina · May 8, 2026, 10:15am

Hi @cherman2, I fixed the problem. As you said it was an issue with my HPC's file.

Thank you