Kraken2 is not creating a report file

[elliewilson9]

I am trying to create both an output file and report file for a set of paired read data. The script runs and generates the ".output" file but does not create a ".report" file.

Set the path to the Kraken2 executable

Kraken2=/zfs/omics/projects/cevolution/software/kraken2/./kraken2

Set the path to the Kraken2 database

Kraken_DB=/zfs/omics/projects/cevolution/NCBI_Database

Set input directory

Input_Dir=/zfs/omics/projects/cevolution/Trim

Set output directoy

Output_Dir=/zfs/omics/projects/cevolution/Metagenomics/Kraken

ID=$(ls -1 $Input_Dir | grep "UVA|Gent" | grep "woCER1" | sed -n ''$i'p' | cut -d"" -f1,2,3,4,5)

Run kraken2

$Kraken2 --db "$Kraken_DB" --gzip-compressed $Input_Dir/$ID"_R1.fastq.gz" $Input_Dir/$ID"_R2.fastq.gz" --paired --output "$Output_Dir/$ID.kraken2.output" --report "$Output_dir/$ID.kraken2.report"

[jenniferlu717]

I think its the order of parameters. You dont need gzipped compressed option

Place the input filenames at the end of the command line and see if the report generates?