what version of kraken2 are you using?
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I enter the command as follow:
time parallel -j 2 \
"kraken2 --db ${db}/kraken2 --paired temp/qc/{1}_1_kneaddata_paired*.fastq \
--threads 3 --use-names --use-mpa-style --report-zero-counts \
--report temp/kraken2/{1}_report \
--output temp/kraken2/{1}_output" \
::: `tail -n+2 result/metadata.tsv | cut -f 1`
the output only include *_output files and not *_report files, I don't know why , anyone helps? Thanks
could you help me? I have the same problem. How to solve it?
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what version of kraken2 are you using?
I use the version, kraken2=2.0.8, do you mean that I should update the version ?
I use 'conda update kraken2' to solve it