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Katie Lennard, 05/11/2022 07:12 AM

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# Wiki
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# Data location





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





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`/cbio/users/katie/Nono/metagenomics





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` 





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





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





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# YAMP pipeline update





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The YAMP pipeline was updated with:





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





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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 





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``` c





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





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```





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





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``` c





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(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





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





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





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





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Downloading file of size: 15.30 GB





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





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





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





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





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Unable to write to the HUMAnN config file.





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```





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AND





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``` c





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(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





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Download URL: http://huttenhower.sph.harvard.edu/humann2_data/uniprot/uniref_annotated/uniref90_annotated_v201901.tar.gz





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Downloading file of size: 19.31 GB





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19.31 GB 100.00 %   7.56 MB/sec  0 min -0 sec





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Extracting: /cbio/users/katie/Nono/YAMP/assets/data/uniref/uniref90_annotated_v201901.tar.gz





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





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Unable to write to the HUMAnN config file.





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```