Project

General

Profile

Edit History

Wiki » History » Version 5

Katie Lennard, 03/31/2022 03:46 PM

1 1 Katie Lennard 
# Wiki
2 





    3
    
    
    
# Data location





    4
    
    
    





    5
    
    
    
The data was transferred using Globus connect and Ilifu's Globus endpoint from a PC setup in cbio to Ilifu: 





    6
    
    
    





    7
    
    
    
`/cbio/users/katie/Nono/metagenomics





    8
    
    
    
` 





    9
    
    
    





    10
    
    
    
The data has already been cleaned and decontaminated (human) by BGI, who have also performed a full analysis on the data (see files section)





    11
    
    
    





    12
    
    
    
The full BGI results can be found together with the cleaned reads on Ilifu.





    13
    2
    Katie Lennard
    





    14
    
    
    
# YAMP pipeline update





    15
    3
    Katie Lennard
    
The YAMP pipeline was updated with:





    16
    
    
    
1. the latest metaphlan DB, downloaded from https://zenodo.org/record/4629921#.Yji3YxNBzOR





    17
    4
    Katie Lennard
    





    18
    
    
    
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 





    19
    
    
    





    20
    
    
    
``` c





    21
    
    
    
singularity pull docker://biobakery/workflows:3.0.0.a.6.metaphlanv3.0.7





    22
    
    
    





    23
    
    
    
```





    24
    
    
    





    25
    
    
    





    26
    5
    Katie Lennard
    
The command executed, from within the github directory of the latest YAMP (https://github.com/alesssia/YAMP) repo was:





    27
    4
    Katie Lennard
    





    28
    
    
    
``` c





    29
    
    
    
(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





    30
    
    
    
Creating directory to install database: /cbio/users/katie/Nono/YAMP/assets/data/chocophlan





    31
    
    
    
Creating subdirectory to install database: /cbio/users/katie/Nono/YAMP/assets/data/chocophlan/chocophlan





    32
    
    
    
Download URL: http://huttenhower.sph.harvard.edu/humann2_data/chocophlan/full_chocophlan.v296_201901.tar.gz





    33
    
    
    
Downloading file of size: 15.30 GB





    34
    
    
    





    35
    
    
    
8.37 GB 54.74 %   8.16 MB/sec 14 min 28 sec





    36
    
    
    
15.30 GB 100.00 %   8.30 MB/sec  0 min -0 sec         





    37
    
    
    
Extracting: /cbio/users/katie/Nono/YAMP/assets/data/chocophlan/full_chocophlan.v296_201901.tar.gz





    38
    
    
    





    39
    
    
    
Database installed: /cbio/users/katie/Nono/YAMP/assets/data/chocophlan/chocophlan





    40
    
    
    





    41
    
    
    
Unable to write to the HUMAnN config file.





    42
    
    
    
```





    43
    
    
    





    44
    
    
    





    45
    3
    Katie Lennard
    
AND





    46
    
    
    
`singularity run biobakery/workflows:3.0.0.a.6.metaphlanv3.0.7 humann_databases --download uniref uniref90_diamond





    47
    1
    Katie Lennard
    
   ./assets/data/uniref`





    48
    5
    Katie Lennard
    





    49
    
    
    
Note that the https://github.com/alesssia/YAMP repo was only used to get the latest metaphlan and humann2 DBs. The pipeline still looked like it doesn't run samples in parallel so we'll stick to our custom version