Unexpected error while finalizing task 'collect_refs' - cause: Unknown variable 'outputDir'

[freya0000]

I am running metacompass in linux terminal. I am not sure why it stops with this error. Could anyone help?

nextflow run [metacompass2.nf](http://metacompass2.nf) \

--reference_db /home/freyajocelyn/S26/2026-04-28/MetaCompass/RefSeq_V2_db \
--forward S40.R1.fq \
--reverse S40.R2.fq \
-output-dir /home/freyajocelyn/S26/2026-04-28/MetaCompass/output \
--trace_file_name "output/trace.txt" \

N E X T F L O W ~ version 25.10.4
Launching [metacompass2.nf](http://metacompass2.nf) [condescending_lorenz] DSL2 - revision: f6e5b1e425
Output dir is /home/freyajocelyn/S26/2026-04-28/MetaCompass/output
executor > local (45)
executor > local (45)
[d2/783dcf] filter_reads | 1 of 1 ✔
[6a/8d043e] map_to_gene (40) | 40 of 40 ✔
[5b/998751] select_genomes | 1 of 1 ✔
[b5/48992a] collect_refs | 0 of 1
[- ] SkaniTriangle | 0 of 1
[- ] Cluster -
[- ] ConcatFasta -
[8c/feaeee] IndexReads | 1 of 1 ✔
[- ] ClusterIndex -
[9a/2087e2] interleaveReads | 1 of 1 ✔
[- ] reduceClusters -
[- ] refAssembly -
[- ] deNovoAssembly -
[- ] createOutputs -
ERROR ~ Unexpected error while finalizing task 'collect_refs' - cause: Unknown variable 'outputDir' -- Make sure it is not misspelled or defined later in the script
-- Check '.nextflow.log' file for details