Open AndreaQ7 opened 1 month ago
It looks like the kaiju profiler option is not set, for some reason...
@AndreaQ7 can you please provide the command that you used to start the pipeline and your database file?
Yes of course, I followed the tutorial: https://nf-co.re/taxprofiler/1.1.8/docs/usage/usage/tutorials/d So the databases are the ones called "test-db-centrifuge.tar.gz" and "test-db-kraken2.tar.gz" and the command line is the one reported in the tutorial
nextflow run nf-core/taxprofiler -r 1.1.0 -profile conda\
--input samplesheet.csv --databases database.csv --outdir ./results \
--perform_shortread_qc \
--perform_shortread_hostremoval --hostremoval_reference GCF_000819615.1_ViralProj14015_genomic.fna.gz \
--perform_runmerging --save_runmerged_reads \
--run_centrifuge --run_kaiju --run_kraken2 \
--run_profile_standardisation \
--max_cpus 2 --max_memory '6.GB'
I just ran the exact same command with the preparatory steps from the tutorial and it completes successfully... So I cannot reproduce your error. Can you please try again from the start? You could also run the latest version -r 1.1.8
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I agree @AndreaQ7 please try with the most recent version of the pipeline. 1.1.0 is very old comparatively :D
Description of the bug
Hello everyone, I am getting the following error during the taxpasta standardise function using the data from the tutorial age: