Kraken2 is not creating a report file
Opened this issue · 1 comments
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 $Input_Dir | grep "UVA|Gent" | grep "woCE_R1" | sed -n ''$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"
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?