Start Taxonomic UniProt                             24-Jan-21 15:38:43
   Check Directories
      Creating directory: ./projects/DBfasta/UniProt_Jan2021
      Creating directory: ./projects/DBfasta/UniProt_Jan2021/sp_bacteria/
      Creating directory: ./projects/DBfasta/UniProt_Jan2021/sp_fungi/
      Creating directory: ./projects/DBfasta/UniProt_Jan2021/sp_invertebrates/
      Creating directory: ./projects/DBfasta/UniProt_Jan2021/sp_plants/
      Creating directory: ./projects/DBfasta/UniProt_Jan2021/sp_viruses/
      Creating directory: ./projects/DBfasta/UniProt_Jan2021/tr_bacteria/
      Creating directory: ./projects/DBfasta/UniProt_Jan2021/tr_fungi/
      Creating directory: ./projects/DBfasta/UniProt_Jan2021/tr_invertebrates/
      Creating directory: ./projects/DBfasta/UniProt_Jan2021/tr_plants/
      Creating directory: ./projects/DBfasta/UniProt_Jan2021/tr_viruses/
   Check complete
   
   Download SwissProt files                             24-Jan-21 15:38:43
      Downloading uniprot_sprot_bacteria.dat.gz
      curl complete ./projects/DBfasta/UniProt_Jan2021/sp_bacteria/uniprot_sprot_bacteria.dat.gz   1m:10s
      Downloading uniprot_sprot_fungi.dat.gz
      curl complete ./projects/DBfasta/UniProt_Jan2021/sp_fungi/uniprot_sprot_fungi.dat.gz   0m:8s
      Downloading uniprot_sprot_invertebrates.dat.gz
      curl complete ./projects/DBfasta/UniProt_Jan2021/sp_invertebrates/uniprot_sprot_invertebrates.dat.gz   0m:12s
      Downloading uniprot_sprot_plants.dat.gz
      curl complete ./projects/DBfasta/UniProt_Jan2021/sp_plants/uniprot_sprot_plants.dat.gz   0m:14s
      Downloading uniprot_sprot_viruses.dat.gz
      curl complete ./projects/DBfasta/UniProt_Jan2021/sp_viruses/uniprot_sprot_viruses.dat.gz   0m:3s
   
   Download TrEMBL files                                24-Jan-21 15:40:32
      Downloading uniprot_trembl_bacteria.dat.gz
      curl complete ./projects/DBfasta/UniProt_Jan2021/tr_bacteria/uniprot_trembl_bacteria.dat.gz   6h:36m:40s
      Downloading uniprot_trembl_fungi.dat.gz
      curl complete ./projects/DBfasta/UniProt_Jan2021/tr_fungi/uniprot_trembl_fungi.dat.gz   26m:23s
      Downloading uniprot_trembl_invertebrates.dat.gz
      curl complete ./projects/DBfasta/UniProt_Jan2021/tr_invertebrates/uniprot_trembl_invertebrates.dat.gz   32m:5s
      Downloading uniprot_trembl_plants.dat.gz
      curl complete ./projects/DBfasta/UniProt_Jan2021/tr_plants/uniprot_trembl_plants.dat.gz   28m:43s
      Downloading uniprot_trembl_viruses.dat.gz
      curl complete ./projects/DBfasta/UniProt_Jan2021/tr_viruses/uniprot_trembl_viruses.dat.gz   13m:35s
   
   Create FASTA files                                   24-Jan-21 23:58:01
      Make FASTA from ./projects/DBfasta/UniProt_Jan2021/sp_bacteria/uniprot_sprot_bacteria.dat.gz
         334,772 written to uniprot_sprot_bacteria.fasta                 0m:24s 
      Make FASTA from ./projects/DBfasta/UniProt_Jan2021/sp_fungi/uniprot_sprot_fungi.dat.gz
         35,073 written to uniprot_sprot_fungi.fasta                     0m:4s  
      Make FASTA from ./projects/DBfasta/UniProt_Jan2021/sp_invertebrates/uniprot_sprot_invertebrates.dat.gz
         28,129 written to uniprot_sprot_invertebrates.fasta             0m:2s  
      Make FASTA from ./projects/DBfasta/UniProt_Jan2021/sp_plants/uniprot_sprot_plants.dat.gz
         43,403 written to uniprot_sprot_plants.fasta                    0m:5s  
      Make FASTA from ./projects/DBfasta/UniProt_Jan2021/sp_viruses/uniprot_sprot_viruses.dat.gz
         17,008 written to uniprot_sprot_viruses.fasta                   0m:1s  
      Make FASTA from ./projects/DBfasta/UniProt_Jan2021/tr_bacteria/uniprot_trembl_bacteria.dat.gz
         140,981,583 written to uniprot_trembl_bacteria.fasta            2h:21m:3s  
      Make FASTA from ./projects/DBfasta/UniProt_Jan2021/tr_fungi/uniprot_trembl_fungi.dat.gz
         12,550,674 written to uniprot_trembl_fungi.fasta                14m:28s  
      Make FASTA from ./projects/DBfasta/UniProt_Jan2021/tr_invertebrates/uniprot_trembl_invertebrates.dat.gz
         12,275,877 written to uniprot_trembl_invertebrates.fasta        13m:22s  
      Make FASTA from ./projects/DBfasta/UniProt_Jan2021/tr_plants/uniprot_trembl_plants.dat.gz
         20,516,158 written to uniprot_trembl_plants.fasta               18m:48s  
      Make FASTA from ./projects/DBfasta/UniProt_Jan2021/tr_viruses/uniprot_trembl_viruses.dat.gz
         4,761,529 written to uniprot_trembl_viruses.fasta               5m:30s  
Complete Taxonomic UniProt                                               11h:33m:10s

Start Full UniProt                                  25-Jan-21 06:08:41
   Check Directories 
      Creating directory: ./projects/DBfasta/UniProt_Jan2021/sp_fullSubset/
   Download SwissProt                                   25-Jan-21 06:08:41
      Downloading uniprot_sprot.dat.gz
      curl complete ./projects/DBfasta/UniProt_Jan2021/sp_fullSubset/uniprot_sprot.dat.gz   1m:16s
   Create subset files                                  25-Jan-21 06:09:57
      Make .dat subset ./projects/DBfasta/UniProt_Jan2021/sp_fullSubset/uniprot_sprot_fullSubset.dat.gz
         Count taxonomic entries
            334,772 IDs in uniprot_sprot_bacteria.fasta
             35,073 IDs in uniprot_sprot_fungi.fasta
             28,129 IDs in uniprot_sprot_invertebrates.fasta
             43,403 IDs in uniprot_sprot_plants.fasta
             17,008 IDs in uniprot_sprot_viruses.fasta
         Allocate memory for 458,385 total entries
         Record taxonomic entries
            458,385 IDs will not be written to subset
         Complete making list                                            0m:4s  
         Sort list
         Write .dat.gz subset file 
            105,587 wrote from 563,972 (19%)                             1m:29s  
      Complete creating .dat subset file                                 1m:36s
      Make FASTA from ./projects/DBfasta/UniProt_Jan2021/sp_fullSubset/uniprot_sprot_fullSubset.dat.gz
         105,587 written to uniprot_sprot_fullSubset.fasta               0m:17s  
Complete Full UniProt                                                    3m:11s  

Start Full UniProt                                  25-Jan-21 17:46:10
   Check Directories 
      Creating directory: ./projects/DBfasta/UniProt_Jan2021/tr_fullSubset/
   Download TrEMBL                                      25-Jan-21 17:46:10
      Downloading uniprot_trembl.dat.gz
      curl complete ./projects/DBfasta/UniProt_Jan2021/tr_fullSubset/uniprot_trembl.dat.gz   7h:3m:10s
   Create subset files                                  26-Jan-21 07:46:12
      Make .dat subset ./projects/DBfasta/UniProt_Jan2021/tr_fullSubset/uniprot_trembl_fullSubset.dat.gz
         Count taxonomic entries
            140,981,583 IDs in uniprot_trembl_bacteria.fasta.gz
            12,550,674 IDs in uniprot_trembl_fungi.fasta.gz
            12,275,877 IDs in uniprot_trembl_invertebrates.fasta.gz
            20,516,158 IDs in uniprot_trembl_plants.fasta.gz
            4,761,529 IDs in uniprot_trembl_viruses.fasta.gz
         Allocate memory for 191,085,821 total entries
         Record taxonomic entries
            191,085,821 IDs will not be written to subset
         Complete making list                                            1h:34m:4s
         Sort list
         Write .dat.gz subset file 
            18,071,318 wrote from 209,157,139 (9%)                       3h:28m:51s
      Complete creating .dat subset file                                 5h:9m:41s
      Make FASTA from ./projects/DBfasta/UniProt_Jan2021/tr_fullSubset/uniprot_trembl_fullSubset.dat.gz 12.9Gb
         18,071,318 written to uniprot_trembl_fullSubset.fasta 10.3Gb    23m:40s
Complete Full UniProt                                                    5h:33m:22s

## Author's note: typically, the GOdb should be created as the same time as the UniProts.
##  Whereas the UniProt were downloaded two months earlier than the GOs in this log.
##	However, there seems to be some obsolete GOs even if they are downloaded the same day.

Start GO processing go_Mar2021                      28-Mar-21 14:17:15
   UniProt directory: ./projects/DBfasta/UniProt_Jan2021
   GO temporary directory: ./projects/DBfasta/GO_oboMar2021
   Delete mySQL database go_Mar2021
   URL: http://current.geneontology.org/ontology/
         50,514 Total GOs     3,305 Alt GOs    3,125 Obsolete
         32,542 Biological   56,609 is_a       5,533 part_of 
         13,289 Molecular    15,018 is_a          11 part_of 
          4,683 Cellular      5,127 is_a       2,097 part_of 
             14 Slims           208 GOs in Slim
   Complete Load OBO file                                                0m:6s  (12Mb)
   Loading ./projects/DBfasta/UniProt_Jan2021 to go_Mar2021
      Processing sp_bacteria/uniprot_sprot_bacteria.dat.gz
               334,772 UniProts   5 Obsolete GOs                         1m:16s  (12Mb)
      Processing sp_fungi/uniprot_sprot_fungi.dat.gz       
                35,073 UniProts  18 Obsolete GOs                         0m:9s  (12Mb)
      Processing sp_invertebrates/uniprot_sprot_invertebrates.dat.gz       
                28,129 UniProts   8 Obsolete GOs                         0m:7s  (12Mb)
      Processing sp_plants/uniprot_sprot_plants.dat.gz        
                43,403 UniProts   2 Obsolete GOs                         0m:12s  (12Mb)
      Processing sp_viruses/uniprot_sprot_viruses.dat.gz           
                17,008 UniProts   1 Obsolete GOs                         0m:4s  (12Mb)
      Processing tr_invertebrates/uniprot_trembl_invertebrates.dat.gz           
            12,275,877 UniProts   12 Obsolete GOs                        28m:41s  (12Mb)
      Processing tr_plants/uniprot_trembl_plants.dat.gz              
            20,516,158 UniProts    4 Obsolete GOs                        39m:14s  (12Mb)
      Processing sp_fullSubset/uniprot_sprot_fullSubset.dat.gz
               105,587 UniProts   46 Obsolete GOs                        0m:43s  (12Mb)
      Totals:
         GO: 49,907,782  Pfam: 21,175,254  KEGG: 2,806,531  EC: 3,736,965  InterPro: 56,704,777
   Compute levels
         19,633 Parent-child
        924,561 edges for biological_process; max level 18
         37,471 edges for cellular_component; max level 14
         28,245 edges for molecular_function; max level 13
      Add GO level numbers to term table
   Complete GO Levels                                                    0m:14s  (16Mb)
   Compute ancestors
         50,514 GOs to process ancestors
        676,026 Ancestor paths 
   Complete ancestors                                                    2m:57s  (94Mb)
Complete creating GO database go_Mar2021                                 1h:13m:48s  (94Mb)