BioBakery HPC.md - quadram-institute-bioscience/biobakery-2024 GitHub Wiki

How to run on HPC (offline mode)

Metaphlan4

1. Required inputs:

• Reads-file (single-end or paired-end)

Note: Metaphlan does not use paired-end information​. As a result, the best way to use paired-end sequencing data with Metaphlan4 is to concatenate forward and reverse reads into a single FASTA or FASTQ file.

• Database: METAPHLAN_BOWTIE2_DB=/qib/platforms/Informatics/databases/metaphlan4/

2. Load metaphlan4

source package metaphlan__4.1.1

3. For help

metaphlan --help

4. Run metaphlan

metaphlan reads.fastq \​
    --input_type fastq \​
    -o profile.txt \​
    --bowtie2db /qib/platforms/Informatics/databases/metaphlan4/ \​
    --offline \​
    --unclassified_estimation -t rel_ab

reads.fastq: input file --input_type: input file-type {fastq,fasta,bowtie2out,sam}
-o: output file name --bowtie2db: Metaphlan database
--offline: to run offline, MetaPhlAn will not check for new database updates.
--unclassified_estimation: To get unclassified reads
-t: Type of analysis to perform (rel_ab: profiling a metagenome in terms of relative abundances)

For further help: Biobakery: Metaphlan-4

HuMANN3

1. Required inputs:

• Reads-file (single-end or paired-end)

Note: Metaphlan does not use paired-end information​. As a result, the best way to use paired-end sequencing data with Metaphlan4 is to concatenate forward and reverse reads into a single FASTA or FASTQ file.

• Database:

• bowtie2db:/qib/platforms/Informatics/transfer/outgoing/databases/metaphlan3/201901-v30​
• nucleotide-database: /qib/platforms/Informatics/transfer/outgoing/databases/humann_db/2022/chocophlan
• protein-database: /qib/platforms/Informatics/transfer/outgoing/databases/humann_db/2022/uniref

2. Load metaphlan4

source package e59dcdcb-efe4-4b6c-90fc-f35899b7e1a2

3. For help

humann --help

4. Run humann

humann --input reads.fastq \​
  --input-format fastq -o reads-50k \​
  --metaphlan-options="-t rel_ab​ -–bowtie2db /qib/platforms/Informatics/transfer/outgoing/databases/metaphlan3/201901-v30 –-index mpa_v30_CHOCOPhlAn_201901" \​
  --nucleotide-database /qib/platforms/Informatics/transfer/outgoing/databases/humann_db/2022/chocophlan \​
  --protein-database /qib/platforms/Informatics/transfer/outgoing/databases/humann_db/2022/uniref \
  --search-mode uniref90 \​
  –threads 16 

For further help Biobakey: HuMANN