Running and Verification

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Go to the directory generated after the decompression.

   cd panphlan-3.1

3. Download the macrogenome sample.

   wget https://www.dropbox.com/s/oi26jg0v7ktlavc/panphlan_tutorial_samples.tar.bz2

4. Decompress the sample file.

   tar -xvjf panphlan_tutorial_samples.tar.bz2

5. Download the reference genome.

   python3 panphlan_download_pangenome.py -i Eubacterium_rectale

6. Map the sample to the pan-genome.

   mkdir map_results/
   python3 panphlan_map.py -i samples_fastq/CCMD34381688ST-21-0.fastq --indexes Eubacterium_rectale/Eubacterium_rectale   -p Eubacterium_rectale/Eubacterium_rectale_pangenome.tsv -o map_results/CCMD34381688ST-21-0_erectale.tsv

   If the following information is displayed, the operation is successful:

   

7. Analyze the strain.

   python3 panphlan_profiling.py -i map_results --o_matrix result_profile_erectale.tsv -p Eubacterium_rectale/Eubacterium_rectale_pangenome.tsv --add_ref

   If the following information is displayed, the operation is successful:

   

8. View the generated file.

   cat result_profile_erectale.tsv