Hi, metaphlan is not creating the output txt files, only bowtie2.bz2 file without any error. I am using metaphlan 4 version and the command I am using is:
find host -name “*unmapped.1.fastq” | cut -d “.” -f1 | parallel -j 20 ‘metaphlan {}.unmapped.1.fastq,{}.unmapped.2.fastq --input_type fastq --bowtie2out {}.bowtie2.bz2 --nproc 20 --bowtie2db metaphlan_database --ignore_eukaryotes --ignore_archaea -o {}. output.txt’
What can be the reason?
Help appreciated!