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!
I tried the same code for one sample without parallel processing, and it worked. My guess is that the problem lies in the comma between ‘1’ and ‘2’ fastq files. The code expects the input to be in the fastq format. I also attempted to use space separation, but it still only generates intermediate files and not the ‘output.txt’ file.
Hi @Nelly
I would suggest to run it as:
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 > output.txt’