Wiki¶

Data location¶

The data was transferred using Globus connect and Ilifu's Globus endpoint from a PC setup in cbio to Ilifu:

/cbio/users/katie/Nono/metagenomics


The data has already been cleaned and decontaminated (human) by BGI, who have also performed a full analysis on the data (see files section)

The full BGI results can be found together with the cleaned reads on Ilifu.

YAMP pipeline update¶

The YAMP pipeline was updated with:

1. the latest metaphlan DB, downloaded from https://zenodo.org/record/4629921#.Yji3YxNBzOR

2. the latest humann DBs (chocophlan and uniref), as described here https://github.com/alesssia/YAMP/wiki/Getting-started#notes-on-the-metaphlan-databases and first downloading the relevant singularity container with

singularity pull docker://biobakery/workflows:3.0.0.a.6.metaphlanv3.0.7

The command executed, from within the github directory of the latest YAMP repo was:

(base) katiel@compute-004:/cbio/users/katie/Nono/YAMP$ singularity run workflows_3.0.0.a.6.metaphlanv3.0.7.sif humann_databases --download chocophlan full ./assets/data/chocophlan
Creating directory to install database: /cbio/users/katie/Nono/YAMP/assets/data/chocophlan
Creating subdirectory to install database: /cbio/users/katie/Nono/YAMP/assets/data/chocophlan/chocophlan
Download URL: http://huttenhower.sph.harvard.edu/humann2_data/chocophlan/full_chocophlan.v296_201901.tar.gz
Downloading file of size: 15.30 GB

8.37 GB 54.74 %   8.16 MB/sec 14 min 28 sec
15.30 GB 100.00 %   8.30 MB/sec  0 min -0 sec         
Extracting: /cbio/users/katie/Nono/YAMP/assets/data/chocophlan/full_chocophlan.v296_201901.tar.gz

Database installed: /cbio/users/katie/Nono/YAMP/assets/data/chocophlan/chocophlan

Unable to write to the HUMAnN config file.

AND

(base) katiel@compute-102:/cbio/users/katie/Nono/YAMP$ singularity run workflows_3.0.0.a.6.metaphlanv3.0.7.sif humann_databases --download uniref uniref90_diamond ./assets/data/uniref
Download URL: http://huttenhower.sph.harvard.edu/humann2_data/uniprot/uniref_annotated/uniref90_annotated_v201901.tar.gz
Downloading file of size: 19.31 GB

19.31 GB 100.00 %   7.56 MB/sec  0 min -0 sec
Extracting: /cbio/users/katie/Nono/YAMP/assets/data/uniref/uniref90_annotated_v201901.tar.gz

Database installed: /cbio/users/katie/Nono/YAMP/assets/data/uniref/uniref

Unable to write to the HUMAnN config file.