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MetaPhlAn: Difference between revisions
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Added submission part
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= Running MetaPhlAn = <!--T:10--> | = Running MetaPhlAn = <!--T:10--> | ||
Once the database files have been downloaded and extracted, you can submit a job. You may edit the following job submission script | Once the database files have been downloaded and extracted, you can submit a job. You may edit the following job submission script | ||
according to your needs | according to your needs: | ||
{{File | {{File | ||
|name=metaphlan-job.sh | |name=metaphlan-job.sh | ||
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metaphlan metagenome.fastq --input_type fastq -o profiled_metagenome.txt -nproc $SLURM_CPUS_PER_TASK --index mpa_vJan21_CHOCOPhlAnSGB_202103 --bowtie2db $DB_DIR --bowtie2out metagenome.bowtie2.bz2 | metaphlan metagenome.fastq --input_type fastq -o profiled_metagenome.txt -nproc $SLURM_CPUS_PER_TASK --index mpa_vJan21_CHOCOPhlAnSGB_202103 --bowtie2db $DB_DIR --bowtie2out metagenome.bowtie2.bz2 | ||
}} | }} | ||
Then submit the job to the scheduler: | |||
{{Command | |||
|sbatch metaphlan-job.sh | |||
}} | |||
</translate> | </translate> | ||