kraken2 don't output report files
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18 months ago

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

kraken2 • 1.0k views
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what version of kraken2 are you using?

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I use the version, kraken2=2.0.8, do you mean that I should update the version ?

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I use 'conda update kraken2' to solve it

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