Command error:
WARNING: DEPRECATED USAGE: Environment variable SINGULARITYENV_TMPDIR will not be supported in the future, use APPTAINERENV_TMPDIR instead
WARNING: DEPRECATED USAGE: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR will not be supported in the future, use APPTAINERENV_NXF_TASK_WORKDIR instead
WARNING: DEPRECATED USAGE: Environment variable SINGULARITYENV_NXF_DEBUG will not be supported in the future, use APPTAINERENV_NXF_DEBUG instead
usage: filter_gtf_for_genes_in_genome.py [-h] [--gtf GTF] [--fasta FASTA]
[-o OUTPUT]
filter_gtf_for_genes_in_genome.py: error: argument --fasta: expected one argument
Command used and terminal output
No response
Relevant files
#!/usr/bin/bash
eval "$(conda shell.bash hook)"
conda activate nextflow
export DIR=$(pwd)
export JAVA_HOME="/home/juan.jovel/mambaforge/envs/nextflow"
export PATH="$JAVA_HOME/bin:$PATH"
REFS="/work/vetmed_data/jj/db/ensembl/GRCh38/reference_sources"
# Run the Nextflow pipeline with the specified configuration and input
nextflow run /work/vetmed_data/jj/projects/juanJovel/pipelines/nextflow/scrnaseq/scrnaseq/main.nf \
-profile singularity \
-c "${DIR}/jj_arc_scrnaseq.config" \
--input "${DIR}/samplesheet.csv" \
--genome_fasta "${REFS}/Homo_sapiens.GRCh38.dna.primary_assembly.fa" \
--gtf "${REFS}/gencode.v32.primary_assembly.annotation.gtf" \
--outdir "${DIR}/results" \
--aligner alevin \
--protocol 10XV2 \
-resume
I could pinpoint that the problem is in file .command.sh in the working directory. Namely, the PATH of my genome fasta file was not included here:
Description of the bug
I am trying to run the scrnaseq nextflow workflow with the following error message:
ERROR ~ Error executing process > 'NFCORE_SCRNASEQ:SCRNASEQ:GTF_GENE_FILTER ([])'
Caused by: Process
NFCORE_SCRNASEQ:SCRNASEQ:GTF_GENE_FILTER ([])
terminated with an error exit status (2)Command executed:
filter_gtf_for_genes_in_genome.py \ --gtf gencode.v32.primary_assembly.annotation.gtf \ --fasta \ -o []_genes.gtf cat <<-END_VERSIONS > versions.yml "NFCORE_SCRNASEQ:SCRNASEQ:GTF_GENE_FILTER": python: $(python --version | sed 's/Python //g') END_VERSIONS
Command exit status: 2
Command output: (empty)
Command error: WARNING: DEPRECATED USAGE: Environment variable SINGULARITYENV_TMPDIR will not be supported in the future, use APPTAINERENV_TMPDIR instead WARNING: DEPRECATED USAGE: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR will not be supported in the future, use APPTAINERENV_NXF_TASK_WORKDIR instead WARNING: DEPRECATED USAGE: Environment variable SINGULARITYENV_NXF_DEBUG will not be supported in the future, use APPTAINERENV_NXF_DEBUG instead usage: filter_gtf_for_genes_in_genome.py [-h] [--gtf GTF] [--fasta FASTA] [-o OUTPUT] filter_gtf_for_genes_in_genome.py: error: argument --fasta: expected one argument
Command used and terminal output
No response
Relevant files
I could pinpoint that the problem is in file .command.sh in the working directory. Namely, the PATH of my genome fasta file was not included here:
System information
My nextflow version:
MY config file:
params { outdir = "${baseDir}/results" input = "${baseDir}/samplesheet.csv" genome_fasta = "/work/vetmed_data/jj/db/ensembl/GRCh38/reference_sources/Homo_sapiens.GRCh38.dna.primary_assembly.fa" gtf = "/work/vetmed_data/jj/db/ensembl/GRCh38/reference_sources/gencode.v32.primary_assembly.annotation.gtf" aligner = "alevin" protocol = "10XV2" }
singularity { enabled = true }
process { executor = 'slurm' memory = '128 GB' cpus = 24 time = '48h' }
singularity { enabled = true autoMounts = true }
docker { enabled = false }
timeline { enabled = true file = "${params.outdir}/pipeline_timeline.html" overwrite = true }
report { enabled = true file = "${params.outdir}/pipeline_report.html" overwrite = true }
trace { enabled = true file = "${params.outdir}/pipeline_trace.txt" overwrite = true }
params { max_cpus = 24 max_memory = '128 GB' }
executor { queueSize = 100 maxForks = 4 }
workDir = '/work/vetmed_data/jj/projects/juanJovel/pipelines/nextflow/scrnaseq'