--------------- Annotate Sequences ---------------   28-Feb-22 06:29:59

Check database sTCW_demoTra
   sTCW ID:  tra
   Database: NT-sTCW
   Create:   2022-02-28
   User:     cari
   Path:     /Users/cari/Workspace/github/TCW/projects/demoTra
   Database has no annotation.

Checking annoDB files
   DB#1 diamond SP AA: projects/DBfasta/UniProt_demo/sp_plants/uniprot_sprot_plants.fasta
   DB#2 diamond SP AA: projects/DBfasta/UniProt_demo/sp_invertebrates/uniprot_sprot_invertebrates.fasta
   DB#3 diamond SP AA: projects/DBfasta/UniProt_demo/sp_fungi/uniprot_sprot_fungi.fasta
   DB#4 diamond SP AA: projects/DBfasta/UniProt_demo/sp_bacteria/uniprot_sprot_bacteria.fasta
   DB#5 diamond SP AA: projects/DBfasta/UniProt_demo/sp_full/uniprot_sprot_xBFxIxPxxx.fasta
   DB#6 diamond TR AA: projects/DBfasta/UniProt_demo/tr_plants/uniprot_trembl_plants.fasta
   DB#7 diamond TR AA: projects/DBfasta/UniProt_demo/tr_invertebrates/uniprot_trembl_invertebrates.fasta
   Pairs blastn: projects/demoTra/hitResults/tra_seqNT.fa
   Pairs tblastx: projects/demoTra/hitResults/tra_seqNT.fa
Checking for existing tab files
Check complete:   Run Search 9   Use existing 0

Check GO database 
   GO database = go_demo
      Valid goDB exists 'go_demo'
      Add GO_slim_subset goslim_plant
Start annotating sequences                           28-Feb-22 06:29:59
   211 Sequences loaded 
   Remove {ECO...} from UniProt descriptions
   Annotate sequences with sequence hits from 7 DB file(s)
         Creating /Users/cari/Workspace/github/TCW/projects/demoTra/hitResults directory
         Create sequence file: projects/demoTra/hitResults/tra_seqNT.fa
            Wrote 211 sequence records
      DB#1 uniprot_sprot_plants.fasta 1.7Mb       28-Feb-22 06:29:59
         Using existing formated files
         Ext/mac/diamond/diamond blastx -q projects/demoTra/hitResults/tra_seqNT.fa -d projects/DBfasta/UniProt_demo/sp_plants/uniprot_sprot_plants.fasta.dmnd -o projects/demoTra/hitResults/tra_SPpla.dmnd.tab --masking 0 -p 24 --quiet
         Complete diamond                                                0m:0s
      DB#1 hits: tra_SPpla.dmnd.tab
           2,959 seq-hit pairs
             193 annotated sequences                                     0m:0s  (3Mb)
      DB#1 descriptions: uniprot_sprot_plants.fasta
           1,344 unique hits descriptions added from 2,775               0m:0s  (2Mb)
      Complete adding DB#1                                               0m:1s

      DB#2 uniprot_sprot_invertebrates.fasta 1.5Mb       28-Feb-22 06:30:01
         Using existing formated files
         Ext/mac/diamond/diamond blastx -q projects/demoTra/hitResults/tra_seqNT.fa -d projects/DBfasta/UniProt_demo/sp_invertebrates/uniprot_sprot_invertebrates.fasta.dmnd -o projects/demoTra/hitResults/tra_SPinv.dmnd.tab --masking 0 -p 24 --quiet
         Complete diamond                                                0m:0s
      DB#2 hits: tra_SPinv.dmnd.tab
           1,271 seq-hit pairs
             126 annotated sequences                                     0m:0s  (2Mb)
      DB#2 descriptions: uniprot_sprot_invertebrates.fasta
             624 unique hits descriptions added from 2,188               0m:0s  (2Mb)
      Complete adding DB#2                                               0m:0s

      DB#3 uniprot_sprot_fungi.fasta 1.6Mb       28-Feb-22 06:30:02
         Using existing formated files
         Ext/mac/diamond/diamond blastx -q projects/demoTra/hitResults/tra_seqNT.fa -d projects/DBfasta/UniProt_demo/sp_fungi/uniprot_sprot_fungi.fasta.dmnd -o projects/demoTra/hitResults/tra_SPfun.dmnd.tab --masking 0 -p 24 --quiet
         Complete diamond                                                0m:0s
      DB#3 hits: tra_SPfun.dmnd.tab
           1,516 seq-hit pairs
             121 annotated sequences                                     0m:0s  (2Mb)
      DB#3 descriptions: uniprot_sprot_fungi.fasta
             895 unique hits descriptions added from 2,349               0m:0s  (2Mb)
      Complete adding DB#3                                               0m:1s

      DB#4 uniprot_sprot_bacteria.fasta 1.4Mb       28-Feb-22 06:30:03
         Using existing formated files
         Ext/mac/diamond/diamond blastx -q projects/demoTra/hitResults/tra_seqNT.fa -d projects/DBfasta/UniProt_demo/sp_bacteria/uniprot_sprot_bacteria.fasta.dmnd -o projects/demoTra/hitResults/tra_SPbac.dmnd.tab --masking 0 -p 24 --quiet
         Complete diamond                                                0m:0s
      DB#4 hits: tra_SPbac.dmnd.tab
           1,126 seq-hit pairs
              63 annotated sequences                                     0m:0s  (2Mb)
      DB#4 descriptions: uniprot_sprot_bacteria.fasta
             790 unique hits descriptions added from 2,176               0m:0s  (2Mb)
      Complete adding DB#4                                               0m:1s

      DB#5 uniprot_sprot_xBFxIxPxxx.fasta 2.6Mb       28-Feb-22 06:30:04
         Using existing formated files
         Ext/mac/diamond/diamond blastx -q projects/demoTra/hitResults/tra_seqNT.fa -d projects/DBfasta/UniProt_demo/sp_full/uniprot_sprot_xBFxIxPxxx.fasta.dmnd -o projects/demoTra/hitResults/tra_SPful.dmnd.tab --masking 0 -p 24 --quiet
         Complete diamond                                                0m:0s
      DB#5 hits: tra_SPful.dmnd.tab
           1,742 seq-hit pairs
             144 annotated sequences                                     0m:0s  (2Mb)
      DB#5 descriptions: uniprot_sprot_xBFxIxPxxx.fasta
             740 unique hits descriptions added from 3,546               0m:0s  (2Mb)
      Complete adding DB#5                                               0m:1s

      DB#6 uniprot_trembl_plants.fasta 10.3Mb       28-Feb-22 06:30:05
         Using existing formated files
         Ext/mac/diamond/diamond blastx -q projects/demoTra/hitResults/tra_seqNT.fa -d projects/DBfasta/UniProt_demo/tr_plants/uniprot_trembl_plants.fasta.dmnd -o projects/demoTra/hitResults/tra_TRpla.dmnd.tab --masking 0 -p 24 --quiet
         Complete diamond                                                0m:0s
      DB#6 hits: tra_TRpla.dmnd.tab
           5,235 seq-hit pairs
             210 annotated sequences                                     0m:0s  (3Mb)
      DB#6 descriptions: uniprot_trembl_plants.fasta
           4,614 unique hits descriptions added from 15,124              0m:3s  (3Mb)
      Complete adding DB#6                                               0m:4s

      DB#7 uniprot_trembl_invertebrates.fasta 9.9Mb       28-Feb-22 06:30:10
         Using existing formated files
         Ext/mac/diamond/diamond blastx -q projects/demoTra/hitResults/tra_seqNT.fa -d projects/DBfasta/UniProt_demo/tr_invertebrates/uniprot_trembl_invertebrates.fasta.dmnd -o projects/demoTra/hitResults/tra_TRinv.dmnd.tab --masking 0 -p 24 --quiet
         Complete diamond                                                0m:0s
      DB#7 hits: tra_TRinv.dmnd.tab
           3,700 seq-hit pairs
             181 annotated sequences                                     0m:0s  (3Mb)
      DB#7 descriptions: uniprot_trembl_invertebrates.fasta
           2,950 unique hits descriptions added from 14,024              0m:2s  (3Mb)
      Complete adding DB#7                                               0m:3s

      Process all hits for 210 sequences 
            4 Sequences with hits to multiple frames 
            4 Sequences with hits to different orientations 
      Finish filter                                                      0m:3s  (3Mb)
      Creating species table
         Read species per sequence from database
          17,549 total seq-hits                                        
           1,571 total species
         Insert species counts into database
         Insert species totals per database
      Finish creating species table                                      0m:0s  (4Mb)
   Finished 210 annotated  1 unannotated                                 0m:17s
   Annotate with GC and ORF 
      Load all sequence from database
             211 Sequences to process
             210 With hits           1 With no hit
             210 Good hit  (%Sim>=20 || E-value>=1E-10)
              61 Great hit (%Sim>=60 && %Hit>=95)
               6 Hits with stops (find longest non-stop hit region)
      Complete load
      Start computation of coding potential
             204 hit sequences        7 Ignored
         Find longest unique sequences with best hits
               0 Non-unique from longest 204 sequences 
         Train with 204 unique longest sequences (59)
         174,483 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
            Base Frequencies: a:0.265  c:0.235  t:0.265  g:0.235  
         Save training results to database
      Complete training                                                  0m:3s  (4Mb)
      Start ORF computation
         Writing ORF information to database and files in projects/demoTra/orfFiles
      Complete ORF computation                                           0m:1s  (5Mb)
      Save all best ORFs to the database
         Save 1266 all frame ORFs to the database
      Finish saving ORF data                                             0m:0s  (5Mb)
      ORF Stats:   Average length 862
            Has Hit            210  (99.5%)    Both Ends     69  (32.7%)    Multi-frame    4   (1.9%)  
            Is Longest ORF     192  (91.0%)    ORF>=300     190  (90.0%)    Stops in Hit   6   (2.8%)  
            Markov Best Score  210  (99.5%)    ORF=Hit      109  (51.7%)    >=9 Ns in ORF  1    (<1%)  
            All of the above   191  (90.5%)      with Ends   32  (15.2%)                               
         Additional ORF info                   For seqs with hit   210  (99.5%)     ORF=Hit with Ends   32  (15.2%)  
          One End             169  (80.1%)      Both Ends           69  (32.9%)      ORF>=300           31  (96.9%)  
          Markov Good Frame   210  (99.5%)      Markov Good Frame  209  (99.5%)      Markov Good Frame  32 (100.0%)  
          ORF=Hit             109  (51.7%)      Markov Best Score  209  (99.5%)      Markov Best Score  32 (100.0%)  
          ORF~Hit              28  (13.3%)      Is Longest ORF     192  (91.4%)      Is Longest ORF     31  (96.9%)  
          ORF>Hit              69  (32.7%)      Longest & Markov   191  (91.0%)      Longest & Markov   31  (96.9%)  
            with Ends          19   (9.0%)      Not hit frame                 0      Sim>=90            14  (43.8%)  
         Frame: 3(13.3%)  2(19.9%)  1(22.3%)  -1(17.1%)  -2(15.2%)  -3(12.3%) 
      Both Ends:           Has Start and Stop codon
      ORF=Hit with ends:   ORF coordinates=Hit coordinates with ends
      Markov Best Score:   Best score from best ORF for each of 6 frames
      Markov Good Frame:   Score>0 and best score from 6 RFs of selected ORF
      GC Content: 48.65%
   Exceptions: 0
      Wrote 252 ORFs to allGoodORFs.pep.fa and allGoodORFs.scores.txt
   Complete annotation with ORF and GC                                   0m:5s

Finished annotating sequences                                           0m:22s

Start creating Pairs                                 28-Feb-22 06:30:22
   Running pairs blastn 
         Format file for blast
         /Users/cari/Workspace/github/TCW/Ext/mac/blast/makeblastdb -dbtype nucl -in projects/demoTra/hitResults/tra_seqNT.fa
         Complete formatting                                             0m:0s
         /Users/cari/Workspace/github/TCW/Ext/mac/blast/blastn -query projects/demoTra/hitResults/tra_seqNT.fa -db projects/demoTra/hitResults/tra_seqNT.fa -out projects/demoTra/hitResults/tra_self_blastn.tab -outfmt 6 -evalue 1e-05 -max_hsps 1  -max_target_seqs 25 -num_threads 24 
   Complete blastn                                                       0m:0s
   Running pairs tblastx
         Using existing formated files
         /Users/cari/Workspace/github/TCW/Ext/mac/blast/tblastx -query projects/demoTra/hitResults/tra_seqNT.fa -db projects/demoTra/hitResults/tra_seqNT.fa -out projects/demoTra/hitResults/tra_self_tblastx.tab -outfmt 6 -evalue 1e-05 -max_hsps 1  -max_target_seqs 25 -num_threads 24 
   Complete tblastx                                                      0m:0s
   Find pairs to align
        20 Pairs from blastn                
       395 Pairs from tblastx                      
   Aligning best 50 out of 415 pairs, due to Pairs limit in Options
   Finished 50 alignments                                                0m:2s
Finished pairwise comparison                                             0m:3s

Start GO update                                      28-Feb-22 06:30:26
   Create database GO tables
   Computing GOs for:
             211 Sequence
          11,957 Unique hits
   Add GO/Interpro/Kegg/Pfam/EC to unique hits table
      Transferring data from a table with 46,440 entries
          10,332 GO
          10,860 Interpro
           4,575 KEGG
          10,594 PFam
           4,895 EC                                                      0m:0s  (86Mb)
   Build Hit-GO table
      Get Hits  
          10,332 hits to process                                         0m:0s  (89Mb)
      Hit to GO mapping                       
           2,989 assigned GOs                                            0m:2s  (93Mb)
      Insert into Hit-GO table...
          50,459 Hit-GO pairs                                            0m:8s  (93Mb)
      Find all inherited...                     
           6,076 assigned and inherited GOs                              0m:4s  (114Mb)
   Build Seq-GO table ...           
      Insert into Seq-GO table...    
             173 sequences have bestBits or bestAnno with GOs 
              35 sequences do not have bestBits or bestAnno with GOs 
               3 sequences have no GO                                    0m:11s  (114Mb)
      Update database with best Hit with GO per sequence...           
             208 update sequences with best Hit with GO                  0m:0s  (87Mb)
   Build GO tables
      Create graph_path from go_demo for GOs
           6,076 processed                                               0m:3s  (87Mb)
      Create GO information table
           6,076 added unique GOs                                        0m:3s  (87Mb)
      Add Slim Subset goslim_plant
              97 Slims in goslim_plant
              94 Added Slims                                             0m:0s  (86Mb)
Finish GO update                                                         0m:37s

End annotation for demoTra                                              1m:5s