error classifying sequences- 0 sequences classified (-nan%)

[ShailNair]

Hi, I have 8 pairs of shotgun fastq sequences. When I run the classification code i get the following error - Loading database information... done. 0 sequences (0.00 Mbp) processed in 0.010s (0.0 Kseq/m, 0.00 Mbp/m). 0 sequences classified (-nan%) 0 sequences unclassified (-nan%) with 0kb .kraken output file.

Here is the full terminal output

kraken2 --use-names --threads 50 --db /home/mcs/database/kraken2/ --report original_1.tab --paired ../original_1_host_removed_R1.fastq ../original_1_host_removed_R1.fastq > original_1.kraken --use-names --classified-out orig-1_kraken2classified_sequences --use-mpa-style --report-zero-count Loading database information... done. 0 sequences (0.00 Mbp) processed in 0.006s (0.0 Kseq/m, 0.00 Mbp/m). 0 sequences classified (-nan%) 0 sequences unclassified (-nan%)

If I use gzip-compressed files instead of fastq I get error- No such file or directory although, the files are right in the same directory kraken2 --use-names --threads 50 --db /home/mcs/database/kraken2 --gzip-compressed --paired ../Original.bottle.1.clean.R1.fastq.gz ../Original.bottle.1.clean.R2.fastq.gz > original_1.kraken --report orig_1.tab --classified-out orig-1_kraken2classified_sequences --use-mpa-style --report-zero-counts

The content of the same path: ls New folder Original.bottle.2.clean.R2.fastq.gz suc.culture.250.days.1.clean.R2.fastq.gz suc.culture.400.days.2.clean.R2.fastq.gz orig_1.tab suc.culture.100.days.1.clean.R1.fastq.gz suc.culture.250.days.2.clean.R1.fastq.gz suc.culture.450.days.1.clean.R1.fastq.gz original_1.kraken suc.culture.100.days.1.clean.R2.fastq.gz suc.culture.250.days.2.clean.R2.fastq.gz suc.culture.450.days.1.clean.R2.fastq.gz Original.bottle.1.clean.R1.fastq.gz suc.culture.100.days.2.clean.R1.fastq.gz suc.culture.400.days.1.clean.R1.fastq.gz suc.culture.450.days.2.clean.R1.fastq.gz Original.bottle.1.clean.R2.fastq.gz suc.culture.100.days.2.clean.R2.fastq.gz suc.culture.400.days.1.clean.R2.fastq.gz suc.culture.450.days.2.clean.R2.fastq.gz Original.bottle.2.clean.R1.fastq.gz suc.culture.250.days.1.clean.R1.fastq.gz suc.culture.400.days.2.clean.R1.fastq.gz

[jenniferlu717]

The sequence files and the pipe to the original_1.kraken file should be at the end of the command line.

In other words, provide all options (--use-mpa-style, --report-zero-counts) before you provide the two sample files and then the > original_1.kraken