--------------- Annotate Sequences 3.0.3---------------   12-Jun-20 12:47:51

Check database sTCW_demoTra
   sTCW ID:      tra
   Create:       2020-05-20
   User Name:    cari
   Project Path: /Users/cari/Workspace/TCW_3/projects/demoTra
   Database has no annotation.

Checking blast and annoDB fasta files
   1. diamond SwissProt Fasta File: projects/DBfasta/UniProt_demo/sp_plants/uniprot_sprot_plants.fasta
   2. diamond SwissProt Fasta File: projects/DBfasta/UniProt_demo/sp_invertebrates/uniprot_sprot_invertebrates.fasta
   3. diamond SwissProt Fasta File: projects/DBfasta/UniProt_demo/sp_fungi/uniprot_sprot_fungi.fasta
   4. diamond SwissProt Fasta File: projects/DBfasta/UniProt_demo/sp_bacteria/uniprot_sprot_bacteria.fasta
   5. diamond SwissProt Fasta File: projects/DBfasta/UniProt_demo/sp_fullSubset/uniprot_sprot_fullSubset.fasta
   6. diamond Trembl Fasta File: projects/DBfasta/UniProt_demo/tr_plants/uniprot_trembl_plants.fasta
   7. diamond Trembl Fasta File: projects/DBfasta/UniProt_demo/tr_invertebrates/uniprot_trembl_invertebrates.fasta
   Create pairs self blast
   Create pairs translated self blast
Complete check files

Check GO database 
   GO database = go_demo
      Add GO terms
Start annotating sequences                           12-Jun-20 12:47:56
   211 Sequences loaded 
   Annotate sequences with sequence hits from 7 DB file(s)
         Creating /Users/cari/Workspace/TCW_3/projects/demoTra/hitResults directory
         Create sequence file: /projects/demoTra/hitResults/tra_sequences.fa
            Wrote 211 sequence records
      DB#1 uniprot_sprot_plants.fasta 2Mb       12-Jun-20 12:47:56
         Using existing formated files
         Ext/mac/diamond/diamond blastx -q /Users/cari/Workspace/TCW_3/projects/demoTra/hitResults/tra_sequences.fa -d /Users/cari/Workspace/TCW_3/projects/DBfasta/UniProt_demo/sp_plants/uniprot_sprot_plants.fasta -o /Users/cari/Workspace/TCW_3/projects/demoTra/hitResults/tra_SPpla.dmnd.tab --masking 0 --max-hsps 1 --top 20 -p 4
         Complete diamond                                                0m:0s
      DB#1 hits: tra_SPpla.dmnd.tab
         193 annotated sequences                                         0m:0s  (4Mb)
         1248 protein-sequence additional pairs 
      DB#1 descriptions: uniprot_sprot_plants.fasta
         747 unique hits descriptions added from 2933                    0m:0s  (8Mb)
         Update hit coverage 

      DB#2 uniprot_sprot_invertebrates.fasta 2Mb       12-Jun-20 12:47:57
         Using existing formated files
         Ext/mac/diamond/diamond blastx -q /Users/cari/Workspace/TCW_3/projects/demoTra/hitResults/tra_sequences.fa -d /Users/cari/Workspace/TCW_3/projects/DBfasta/UniProt_demo/sp_invertebrates/uniprot_sprot_invertebrates.fasta -o /Users/cari/Workspace/TCW_3/projects/demoTra/hitResults/tra_SPinv.dmnd.tab --masking 0 --max-hsps 1 --top 20 -p 4
         Complete diamond                                                0m:0s
      DB#2 hits: tra_SPinv.dmnd.tab
         121 annotated sequences                                         0m:0s  (4Mb)
         482 protein-sequence additional pairs 
      DB#2 descriptions: uniprot_sprot_invertebrates.fasta
         285 unique hits descriptions added from 2403                    0m:0s  (5Mb)
         Update hit coverage 

      DB#3 uniprot_sprot_fungi.fasta 2Mb       12-Jun-20 12:47:58
         Using existing formated files
         Ext/mac/diamond/diamond blastx -q /Users/cari/Workspace/TCW_3/projects/demoTra/hitResults/tra_sequences.fa -d /Users/cari/Workspace/TCW_3/projects/DBfasta/UniProt_demo/sp_fungi/uniprot_sprot_fungi.fasta -o /Users/cari/Workspace/TCW_3/projects/demoTra/hitResults/tra_SPfun.dmnd.tab --masking 0 --max-hsps 1 --top 20 -p 4
         Complete diamond                                                0m:0s
      DB#3 hits: tra_SPfun.dmnd.tab
         112 annotated sequences                                         0m:0s  (4Mb)
         947 protein-sequence additional pairs 
      DB#3 descriptions: uniprot_sprot_fungi.fasta
         566 unique hits descriptions added from 2416                    0m:0s  (7Mb)
         Update hit coverage 

      DB#4 uniprot_sprot_bacteria.fasta 1Mb       12-Jun-20 12:47:59
         Using existing formated files
         Ext/mac/diamond/diamond blastx -q /Users/cari/Workspace/TCW_3/projects/demoTra/hitResults/tra_sequences.fa -d /Users/cari/Workspace/TCW_3/projects/DBfasta/UniProt_demo/sp_bacteria/uniprot_sprot_bacteria.fasta -o /Users/cari/Workspace/TCW_3/projects/demoTra/hitResults/tra_SPbac.dmnd.tab --masking 0 --max-hsps 1 --top 20 -p 4
         Complete diamond                                                0m:0s
      DB#4 hits: tra_SPbac.dmnd.tab
         59 annotated sequences                                          0m:0s  (4Mb)
         819 protein-sequence additional pairs 
      DB#4 descriptions: uniprot_sprot_bacteria.fasta
         532 unique hits descriptions added from 2020                    0m:0s  (7Mb)
         Update hit coverage 

      DB#5 uniprot_sprot_fullSubset.fasta 4Mb       12-Jun-20 12:47:59
         Using existing formated files
         Ext/mac/diamond/diamond blastx -q /Users/cari/Workspace/TCW_3/projects/demoTra/hitResults/tra_sequences.fa -d /Users/cari/Workspace/TCW_3/projects/DBfasta/UniProt_demo/sp_fullSubset/uniprot_sprot_fullSubset.fasta -o /Users/cari/Workspace/TCW_3/projects/demoTra/hitResults/tra_SPful.dmnd.tab --masking 0 --max-hsps 1 --top 20 -p 4
         Complete diamond                                                0m:0s
      DB#5 hits: tra_SPful.dmnd.tab
         134 annotated sequences                                         0m:0s  (4Mb)
         1361 protein-sequence additional pairs 
      DB#5 descriptions: uniprot_sprot_fullSubset.fasta
         686 unique hits descriptions added from 5360                    0m:0s  (8Mb)
         Update hit coverage 

      DB#6 uniprot_trembl_plants.fasta 10Mb       12-Jun-20 12:48:01
         Using existing formated files
         Ext/mac/diamond/diamond blastx -q /Users/cari/Workspace/TCW_3/projects/demoTra/hitResults/tra_sequences.fa -d /Users/cari/Workspace/TCW_3/projects/DBfasta/UniProt_demo/tr_plants/uniprot_trembl_plants.fasta -o /Users/cari/Workspace/TCW_3/projects/demoTra/hitResults/tra_TRpla.dmnd.tab --masking 0 --max-hsps 1 --top 20 -p 4
         Complete diamond                                                0m:1s
      DB#6 hits: tra_TRpla.dmnd.tab
         209 annotated sequences                                         0m:1s  (4Mb)
         4723 protein-sequence additional pairs 
      DB#6 descriptions: uniprot_trembl_plants.fasta
         4056 unique hits descriptions added from 13890                  0m:2s  (28Mb)
         Update hit coverage 

      DB#7 uniprot_trembl_invertebrates.fasta 5Mb       12-Jun-20 12:48:06
         Using existing formated files
         Ext/mac/diamond/diamond blastx -q /Users/cari/Workspace/TCW_3/projects/demoTra/hitResults/tra_sequences.fa -d /Users/cari/Workspace/TCW_3/projects/DBfasta/UniProt_demo/tr_invertebrates/uniprot_trembl_invertebrates.fasta -o /Users/cari/Workspace/TCW_3/projects/demoTra/hitResults/tra_TRinv.dmnd.tab --masking 0 --max-hsps 1 --top 20 -p 4
         Complete diamond                                                0m:0s
      DB#7 hits: tra_TRinv.dmnd.tab
         163 annotated sequences                                         0m:0s  (5Mb)
         2425 protein-sequence additional pairs 
      DB#7 descriptions: uniprot_trembl_invertebrates.fasta
         1644 unique hits descriptions added from 6884                   0m:1s  (14Mb)
         Update hit coverage 

      Process all hits for 209 sequences 
            3 Sequences with hits to multiple frames 
      Finish filter                                                      0m:2s  (5Mb)
      Creating species table
         Read species per sequence from database (1,211)
                12k  total hits                                        
               992   total species
         Insert species counts into database
         Insert species totals per database
      Finish creating species table                                      0m:0s  (5Mb)

   Finished 209 annotated  2 unannotated                                 0m:15s
   Annotate  with GC and ORF
      ### Use ATG only for start site
      ### Rule 1: Use Good hit: E-value <=1E-10 or Sim >= 20%
      ### Rule 2: Use longest ORF if Log Len Ratio > 0.5
      ### Rule 3: Use best Markov score
      ###         Train using best hits
      ### Good coverage: Hit overlap >= 95% with Sim 60% (internal params)

      Load all sequence from database
             211 Sequences to process
               2 Sequences with no hits 
             209 Sequences with hit
             209 Good hit
              59 Good coverage 
               5 Hits with stops, find longest non-Stop region in hit
      Complete load
      Start computation of coding potential
         Train and write hit regions to /projects/demoTra/orfFiles/hitRegions.fa
             204 Sequences used for training 
            175k Bases used for training
         Compute Codon frequency and write to /projects/demoTra/orfFiles/scoreCodon.txt
         Compute Markov loglikelihood and write to /projects/demoTra/orfFiles/scoreMarkov.txt
         Save training results to database
      Complete training                                                  0m:3s  (6Mb)
      Start ORF computation
      Writing ORF information to database and files in /projects/demoTra/orfFiles
      Complete ORF computation                                           0m:0s  (6Mb)

      Save all best ORFs to the database
      Save 1266 all frame ORFs to the database
      Finish saving ORF data                                             0m:0s  (6Mb)
      Total ORFs: 211 (100.0%)
            Has Hit             209 (99.1%)    ORF>=300         191 (90.5%)    MultiFrame     3  (1.4%)  
            Is Longest ORF      200 (94.8%)    Has Start&Stop    53 (25.1%)    >=9 Ns in ORF  0    (0%)  
            Markov Best Score  211 (100.0%)    Has Start|Stop   164 (77.7%)    Stops in Hit   5  (2.4%)  
            All of the above    199 (94.3%)    Average ORF len         860         
            Additional ORF info                   For seqs with hit           209     Hit w/good coverage           59  
            Markov Good Frame    211 (100.0%)     Longest & Markov    199 (95.2%)     Longest & Markov     59 (100.0%)  
            ORF=Hit               123 (58.3%)     Is Longest ORF      199 (95.2%)     Is Longest ORF       59 (100.0%)  
            ORF>Hit                76 (36.0%)     Markov Best Score  209 (100.0%)     Markov Best Score    59 (100.0%)  
            ORF~Hit                10  (4.7%)     Markov Good Frame  209 (100.0%)     Markov Good Frame    59 (100.0%)  
            ORF>Hit & HasEnds      21 (10.0%)     Has Start & Stop     53 (25.4%)     Has Start & Stop      45 (76.3%)  
            ORF=Hit & HasEnds      30 (14.2%)     Not hit frame                 0     ORF=Hit & HasEnds     29 (49.2%)  
         Frame: 3(13.3%)  2(19.9%)  1(22.3%)  -1(17.1%)  -2(15.2%)  -3(12.3%) 
      GC Content: 48.65%
            Pos1  18.3%              5UTR    CDS   3UTR              5UTR     CDS    3UTR  
            Pos2  13.7%    %GC      43.91  48.78  36.27    Length     22k    181k     25k  
            Pos3  16.6%    CpG-O/E   0.88   0.71   0.63    AvgLen   102.3   859.7   117.1  
      Wrote 41 ORFs to allGoodORFs.pep.fa and allGoodORFs.scores.txt
   Complete annotation with ORF and GC                                   0m:4s

Finished annotating sequences                                           0m:20s

Start sequence comparisons                           12-Jun-20 12:48:16
   Running Sequence selfblast 
         Format file for blast
         Ext/mac/blast/makeblastdb -dbtype nucl -in /Users/cari/Workspace/TCW_3/projects/demoTra/hitResults/tra_sequences.fa
         Complete formatting                                             0m:0s
         Ext/mac/blast/blastn -query /Users/cari/Workspace/TCW_3/projects/demoTra/hitResults/tra_sequences.fa -db /Users/cari/Workspace/TCW_3/projects/demoTra/hitResults/tra_sequences.fa -out /Users/cari/Workspace/TCW_3/projects/demoTra/hitResults/tra_blast_self.tab -outfmt 6 -evalue 1e-20 -max_hsps 1 -num_threads 4 
Complete blastn                                      12-Jun-20 12:48:16   0m:0s
   Running Sequence translated selfblast
         Using existing formated files
         Ext/mac/blast/tblastx -query /Users/cari/Workspace/TCW_3/projects/demoTra/hitResults/tra_sequences.fa -db /Users/cari/Workspace/TCW_3/projects/demoTra/hitResults/tra_sequences.fa -out /Users/cari/Workspace/TCW_3/projects/demoTra/hitResults/tra_blast_tself.tab -outfmt 6 -evalue 1e-05 -max_hsps 1 -max_target_seqs 25 -num_threads 4 
Complete tblastx                                     12-Jun-20 12:48:17   0m:1s
   Find pairs to align
      415 Pairs from tblastx self-blast 
        0 Additional pairs from self-blast 
      415 Total unique pairs 
   Aligning best 30 out of 415 pairs, due to Pairs limit in Options
Finished 30 sequence comparisons                                         0m:3s

Start GO update                                      12-Jun-20 12:48:20
   Create database GO tables
   Computing GOs for:
             211 Sequence
           8,516 Unique hits
   Add GO/Interpro/Kegg/Pfam/EC to unique hits table
           8,088 GO
           8,324 Interpro
           3,932 KEGG
           8,161 PFam
           3,419 EC                                                      0m:0s  (87Mb)
   Build hit-GO table
      Get hits  
           8,088 hits to process                                         0m:0s  (91Mb)
      Hit to GO mapping                       
           2,223 assigned GOs                                            0m:1s  (93Mb)
      Insert into hit-go table...
          37,418 hit-GO pairs                                            0m:6s  (93Mb)
      Find all inherited...                     
           5,002 assigned and inherited GOs                              0m:3s  (111Mb)
   Build Seq-GO table ...           
      Insert into seq-go table...    
             200 sequences have bestEval or bestAnno with GOs 
               7 sequences do not have bestEval or bestAnno with GOs 
               4 sequences have no GO                                    0m:8s  (111Mb)
      Update database with best Hit with GO per sequence...           
             207  update sequences with best Hit with GO                 0m:0s  (88Mb)
   Build GO tables
      Create graph_path from go_demo for GOs
           5,002  processed                                              0m:3s  (88Mb)
      Create GO information table
           5,002 added unique GOs                                        0m:9s  (88Mb)
      Create GO tree
          93,395 branches                                                0m:3s  (87Mb)
Finish GO update                                                         0m:37s
Complete Overview                                                        0m:0s

End annotation for demoTra                                              1m:7s