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Hi! I am getting an error trying to run kraken2 on...
# taxprofiler
i
Hi! I am getting an error trying to run kraken2 on nanopore fasta files:
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ERROR ~ Error executing process > 'NFCORE_TAXPROFILER:taxprofiler:PROFILING:KRAKEN2_KRAKEN2 (6)'
Caused by:
  Not a valid path value type: java.util.ArrayList ([])
My command (running taxprofiler v1.1.8):
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nextflow run <http://main.nf|main.nf> \
    -profile docker \
    --input samplesheet.csv \
    --databases databases.csv \
    --outdir /Users/user/Documents/emu/Development/taxprofiler \
    --skip_preprocessing_qc \
    --run_kraken2 \
    --run_profile_standardisation \
    --taxpasta_taxonomy_dir /Users/user/Documents/databases/taxdump \
    --taxpasta_add_name
My sample sheet:
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sample,run_accession,instrument_platform,fastq_1,fastq_2,fasta
barcode25,v0.1.0_unclassified,OXFORD_NANOPORE,,,/Users/user/Documents/emu/Development/test/barcode25_unclassified.fa.gz
barcode26,v0.1.0_unclassified,OXFORD_NANOPORE,,,/Users/user/Documents/emu/Development/test/barcode26_unclassified.fa.gz
barcode33,v0.1.0_unclassified,OXFORD_NANOPORE,,,/Users/user/Documents/emu/Development/test/barcode33_unclassified.fa.gz
However, it works if I pretend I have illumina data - replacing 
OXFORD_NANOPORE
with 
ILLUMINA
in the sample sheet 🤔
🤔 1
j
Let me try and replicate
I'm not getting this error when I basically do the same thing as you 🤔
What does the databases.csv look like?
Also I note your error looks weird (the lower case taxprofiler), are you running on afork?
As in I ran
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nextflow run ../main.nf -profile docker --input samplesheet.csv --databases database_v1.1_local.csv --outdir ./results --skip_preprocessing_qc --run_kraken2 --run_profile_standardisation --max_memory 6.GB
Where samplesheet is:
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sample,run_accession,instrument_platform,fastq_1,fastq_2,fasta
ERR3201952,ERR3201952,OXFORD_NANOPORE,<https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERR3201952.fastq.gz>,,
OH NO WAIT FASTA not FASTQ
ok replicated 🙂 can investigate now
OK I'm lost...
(technical description): Basically somehow the path to the FASTA file is being lost between the samplesheet 
.branch
and then mixing into the reads channel that going into PROFILING
AHHH FOUND IT
@Ida Karlsson do you have a GitHub handle?
(we thank bug reporters in our changelog 🙂 )
i
Ok, good it’s sorted out! On Github I am ikarls
j
I just made a PR, might be a few days until we get a release though (Just FYI)
👍 1
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