#C02FC6VFQG1 Hello, I got the below execution report after I ran this command line: nextflow run nf-core/metatdenovo -profile conda --input samplesheet.csv --assembler megahit --save_bam --save_samtools --orf_caller prokka --eukulele_dbpath path/to/db /home/nspmpego/microbiota_photoperiodism/metatranscriptomics/eggnog/ --outdir results/ --email "myemail". Is the command ok? I am unsure about the --eukelele_path command. What does the error in the execution report mean, and how can I fix it? Any help would be greatly appreciated. The exit status of the task that caused the workflow execution to fail was: null.
The full error message was:
Error executing process > 'NFCORE_METATDENOVO
METATDENOVOSUB_EUKULELE:EUKULELE_SEARCH (megahit.prokka)'
Caused by:
Process exceeded running time limit (16h)
Command executed:
rc=0
mkdir contigs
gunzip -c prokka.faa.gz > ./contigs/proteins.faa
EUKulele \
-m mets \
\
--protein_extension .faa \
--reference_dir db \
-o megahit.prokka_[] \
--CPUs 12 \
-s \
contigs || rc=$?
gzip megahit.prokka_[]/mets_full/diamond/*.out
find megahit.prokka_[]/ -name "*.csv" | xargs gzip
gzip megahit.prokka_[]/taxonomy_estimation/*.out
cat <<-END_VERSIONS > versions.yml
"NFCORE_METATDENOVO
METATDENOVOSUB_EUKULELE:EUKULELE_SEARCH":
eukulele: $(echo $(EUKulele --version 2>&1) | sed -n 's/.* \([0-9]\+\.[0-9]\+\.[0-9]\+\).*/\1/p')
END_VERSIONS
if [ $rc -le 1 ]; then
exit 0
else
exit $rc;
fi
Command exit status:
-
Command output:
(empty)
Work dir:
/home/nspmpego/microbiota_photoperiodism/metatranscriptomics/ld_sd_meta/work/f2/6ff4027d94eb82d726802074e2bd6d
Tip: view the complete command output by changing to the process work dir and entering the command
cat .command.out
The workflow was completed at 2026-05-13T05
2144.895650384+01:00 (duration: 1d 15h 46m 41s) (edited)
execution_report_2026-05-11_13-35-01.html