kraken2 paired end reads not processing

Question

[serene.s]

Hi Everyone!

I am being encountered by an error when I am trying to process the paired-end reads with kraken2, the error is:

kraken2: --paired requires positive and even number filenames

The command that I am giving on the terminal is:

kraken2 --use-names --db /home/rakesh/minikraken_8GB_20200312/ --threads 10 --paired /home/rakesh/Subsampled_70bp_fastq/A1_R1.fq.gz /home/rakesh/Subsampled_70bp_fastq/A1_R2.fq.gz --report /home/rakesh/Documents/Kraken_out/A1_report --use-mpa-style /home/rakesh/Documents/Kraken_out/A1_mpa_style_rep --gzip-compressed

Kindly help me resolve the issue.

Thanks

[shenwei356]

The flag --use-mpa-style should not be followed with any values.

  --use-mpa-style         With --report, format report output like Kraken 1's
                          kraken-mpa-report