Start Taxonomic UniProt 20-Dec-21 16:47:15
Check Directories
Creating directory: projects/DBfasta/UniProt_Dec2021
Creating directory: projects/DBfasta/UniProt_Dec2021/sp_fungi/
Creating directory: projects/DBfasta/UniProt_Dec2021/sp_plants/
Check complete
Download SwissProt files 20-Dec-21 16:47:15
Downloading uniprot_sprot_fungi.dat.gz
curl complete projects/DBfasta/UniProt_Dec2021/sp_fungi/uniprot_sprot_fungi.dat.gz 0m:10s
Downloading uniprot_sprot_plants.dat.gz
curl complete projects/DBfasta/UniProt_Dec2021/sp_plants/uniprot_sprot_plants.dat.gz 0m:9s
Complete SwissProt download 0m:20s
Create FASTA files 20-Dec-21 16:47:36
Create SP FASTA from projects/DBfasta/UniProt_Dec2021/sp_fungi/uniprot_sprot_fungi.dat.gz (Size 52.6Mb)
35,623 of 35,623 written to uniprot_sprot_fungi.fasta
Complete SP FASTA file 0m:1s (6Mb)
Create SP FASTA from projects/DBfasta/UniProt_Dec2021/sp_plants/uniprot_sprot_plants.dat.gz (Size 53.4Mb)
43,739 of 43,739 written to uniprot_sprot_plants.fasta
Complete SP FASTA file 0m:1s (6Mb)
Complete create files 0m:3s
Complete Taxonomic UniProt 0m:23s (6Mb)
Download Full UniProt 20-Dec-21 16:48:18
Check Directories
Download SwissProt 20-Dec-21 16:48:18
Creating directory: projects/DBfasta/UniProt_Dec2021/sp_full/
Downloading uniprot_sprot.dat.gz
curl complete projects/DBfasta/UniProt_Dec2021/sp_full/uniprot_sprot.dat.gz 0m:56s
Complete Full Download 0m:56s
Create Full UniProt Fasta 20-Dec-21 16:49:19
Create SP hitID list from selected fasta files
35,623 IDs in uniprot_sprot_fungi.fasta
43,739 IDs in uniprot_sprot_plants.fasta
79,362 sequences will not be written to subset fasta file
Complete SP hitID list 0m:0s
Create SP FASTA from projects/DBfasta/UniProt_Dec2021/sp_full/uniprot_sprot.dat.gz (Size 625.8Mb)
486,566 of 565,928 written to uniprot_sprot_xxFxxxPxxx.fasta
Complete SP FASTA file 0m:17s (17Mb)
Complete Full UniProt fasta 0m:18s (7Mb)
Start GO processing go_Dec2021 20-Dec-21 16:50:36
UniProt directory: projects/DBfasta/UniProt_Dec2021
GO temporary directory: projects/DBfasta/GO_oboDec2021
URL: http://current.geneontology.org/ontology/
Downloading go-basic.obo
curl complete projects/DBfasta/GO_oboDec2021/go-basic.obo 0m:2s
50,757 Total GOs 3,496 Alt GOs 3,472 Obsolete
32,645 Biological 56,021 is_a 5,417 part_of
13,403 Molecular 15,089 is_a 13 part_of
4,709 Cellular 5,128 is_a 2,092 part_of
14 Slims 225 GOs in Slim
Complete Load OBO file 0m:1s (19Mb)
Loading projects/DBfasta/UniProt_Dec2021 to go_Dec2021
Processing sp_fungi/uniprot_sprot_fungi.dat.gz
35,623 UniProts 31 Obsolete GOs 0m:3s (15Mb)
Processing sp_plants/uniprot_sprot_plants.dat.gz
43,739 UniProts 19 Obsolete GOs 0m:4s (15Mb)
Processing sp_full/uniprot_sprot.dat.gz
486,566 UniProts 74 Obsolete GOs 79,362 Already in GOdb 0m:55s (15Mb)
Totals:
GO: 3,513,268 Pfam: 889,988 KEGG: 554,505 EC: 318,075 InterPro: 2,621,448
Compute levels
18,345 Parent-child
833,504 edges for biological_process; max level 18
41,061 edges for cellular_component; max level 14
25,151 edges for molecular_function; max level 12
Add GO level numbers to term table
Complete GO Levels 0m:10s (23Mb)
Compute ancestors
50,757 GOs to process ancestors
658,497 Ancestor paths
Complete ancestors 2m:2s (100Mb)
Complete creating GO database go_Dec2021 3m:26s (100Mb)
Write projects/AnnoDBs_UniProt_Dec2021.cfg
3 entries written