#~~# #~+~~+~# #~~# #LOG 00:00:00 Activity Log for SLiMSuite V1.5.2: Wed Dec 9 00:29:26 2015 #DIR 00:00:00 Run from directory: /srv/slimsuite/logs/prod #ARG 00:00:00 Commandline arguments: run ip=129.94.133.155 slimfinder&uniprotid=CTBP1&dismask=T&consmask=T&runid=CtBP1-ConsMask&jobid=15120900003 #VIO 00:00:00 Verbosity: -1; Interactivity: -1. #PROG 00:00:00 SLiMFinder V5.2.3: Short Linear Motif Finder #CMD 00:00:00 Full SLiMFinder CmdList: proglog=F iucut=0.2 usegopher=T protscores=T megablam=F orthdb=qfo_ref.2015-04.Eukaryota.fas sourcedate=2015-04-15 walltime=0 maxgapx=3 rest=format uniprotid=CTBP1.hint.acc dismask=T consmask=T runid=CtBP1-ConsMask jobid=15120900003 resfile=slimfinder.csv savespace=0 targz=F megaslim=seqin basefile=slimfinder #DB 00:00:00 /srv/slimsuite/data/orthdb/qfo_ref.2015-04/qfo_ref.2015-04.Eukaryota.fas already formatted. (Force = False). #DB 00:00:00 /srv/slimsuite/data/orthdb/qfo_ref.2015-04/qfo_ref.2015-04.Eukaryota.fas already formatted. (Force = False). #ALPH 00:00:00 Alphabet: A C D E F G H I K L M N P Q R S T V W Y #WARN 00:00:00 NOTE: cloudfix=F. Be wary of ambiguity over-predictions. #URL 00:00:04 Extracting 20 AccNum from http://www.uniprot.org/uniprot/: 20 read & extracted; 0 failed; 0 duplicates. #DAT 00:00:05 Extracting entries from slimfinder.dat: 20 read, 20 extracted. #SEQ 00:00:05 20 sequences loaded from /srv/slimsuite/scratch/prod/slimfinder/15120900003/slimfinder.dat (Format: uniprot). #FAS 00:00:05 20 Sequences output to /srv/slimsuite/scratch/prod/slimfinder/15120900003/slimfinder.fas. #UPC 00:00:05 No UPC file found. #FAS 00:00:05 20 Sequences output to /srv/slimsuite/scratch/prod/slimfinder/15120900003/slimfinder.slimdb. #DICT 00:00:05 Made "short" seqName dictionary: 20 seq; 20 keys. #DB 00:00:05 /share/apps/blast+/2.2.29/bin/makeblastdb -in "/srv/slimsuite/scratch/prod/slimfinder/15120900003/slimfinder.slimdb" -out "/srv/slimsuite/scratch/prod/slimfinder/15120900003/slimfinder.slimdb" -title "/srv/slimsuite/scratch/prod/slimfinder/15120900003/slimfinder.slimdb" -parse_seqids -dbtype prot #SYS 00:00:05 /share/apps/blast+/2.2.29/bin/blastp -query /srv/slimsuite/scratch/prod/slimfinder/15120900003/slimfinder.slimdb -db /srv/slimsuite/scratch/prod/slimfinder/15120900003/slimfinder.slimdb -out /srv/slimsuite/scratch/prod/slimfinder/15120900003/slimfinder.self.blast -seg yes -comp_based_stats F -soft_masking true -evalue 1.000000e-04 -num_descriptions 20 -num_alignments 20 #INDEX 00:00:05 Indexed "Search" on "Query": 20 unique; 0 missing entries #CLUST 00:00:05 16 clusters generated from 20 keys (maxdis=1.00) #DICT 00:00:05 Made "short" seqName dictionary: 20 seq; 20 keys. #MST 00:00:05 MST for 20 sequences = 19.049. #UP 00:00:05 slimfinder: 20 Seq; 16 UPC; 19.049 MST; blaste=1.00e-04, blastcf=F, blastf=T #MAT 00:00:05 slimfinder GABLAM Distance matrix out to /srv/slimsuite/scratch/prod/slimfinder/15120900003/slimfinder.dis.tdt (text format). #MIN 00:00:05 AmbOcc 0.05 & 16 UP => AmbOcc 2 UPC. #MIN 00:00:05 MinOcc 0.05 & 16 UP => MinOcc 3 UPC. #DIS 00:00:05 Disorder score file: /srv/slimsuite/scratch/prod/slimfinder/15120900003/slimfinder.iupred.txt #MASK 00:00:05 ATX1L_HUMAN__P0C7T5 masked 21 ordered regions. (107 X added.) #MASK 00:00:05 BRCA1_HUMAN__P38398 masked 20 ordered regions. (268 X added.) #MASK 00:00:05 CBX4_HUMAN__O00257 masked 3 ordered regions. (54 X added.) #MASK 00:00:05 CHD3_HUMAN__Q12873 masked 58 ordered regions. (747 X added.) #MASK 00:00:05 COM1_HUMAN__Q99708 masked 14 ordered regions. (46 X added.) #MASK 00:00:05 CTBP1_HUMAN__Q13363 masked 13 ordered regions. (221 X added.) #MASK 00:00:05 CTNA1_HUMAN__P35221 masked 33 ordered regions. (329 X added.) #MASK 00:00:05 HDAC2_HUMAN__Q92769 masked 18 ordered regions. (240 X added.) #MASK 00:00:05 HIC1_HUMAN__Q14526 masked 22 ordered regions. (221 X added.) #MASK 00:00:05 IKZF1_HUMAN__Q13422 masked 8 ordered regions. (110 X added.) #MASK 00:00:05 ITF2_HUMAN__P15884 masked 3 ordered regions. (30 X added.) #MASK 00:00:05 KAT2B_HUMAN__Q92831 masked 24 ordered regions. (408 X added.) #MASK 00:00:05 LCORL_HUMAN__Q8N3X6 masked 22 ordered regions. (117 X added.) #MASK 00:00:05 LCOR_HUMAN__Q96JN0 masked 7 ordered regions. (17 X added.) #MASK 00:00:05 MDS1_HUMAN__Q13465 masked 3 ordered regions. (35 X added.) #MASK 00:00:05 NOL4L_HUMAN__Q96MY1 masked 2 ordered regions. (27 X added.) #MASK 00:00:05 NRIP1_HUMAN__P48552 masked 10 ordered regions. (26 X added.) #MASK 00:00:05 RBBP5_HUMAN__Q15291 masked 14 ordered regions. (234 X added.) #MASK 00:00:05 SOBP_HUMAN__A7XYQ1 masked 7 ordered regions. (143 X added.) #MASK 00:00:05 ZN219_HUMAN__Q9P2Y4 masked 15 ordered regions. (96 X added.) #DB 00:00:05 /srv/slimsuite/data/orthdb/qfo_ref.2015-04/qfo_ref.2015-04.Eukaryota.fas already formatted. (Force = False). #MASK 00:00:05 Masked ATX1L_HUMAN__P0C7T5 low relative conservation. (274 X added to 689aa seq.) #MASK 00:00:05 Masked BRCA1_HUMAN__P38398 low relative conservation. (847 X added to 1863aa seq.) #MASK 00:00:05 Masked CBX4_HUMAN__O00257 low relative conservation. (254 X added to 560aa seq.) #MASK 00:00:05 Masked CHD3_HUMAN__Q12873 low relative conservation. (635 X added to 2000aa seq.) #MASK 00:00:05 Masked COM1_HUMAN__Q99708 low relative conservation. (377 X added to 897aa seq.) #MASK 00:00:05 Masked CTBP1_HUMAN__Q13363 low relative conservation. (107 X added to 440aa seq.) #MASK 00:00:05 Masked CTNA1_HUMAN__P35221 low relative conservation. (276 X added to 906aa seq.) #MASK 00:00:05 Masked HDAC2_HUMAN__Q92769 low relative conservation. (126 X added to 488aa seq.) #MASK 00:00:05 Masked HIC1_HUMAN__Q14526 low relative conservation. (238 X added to 733aa seq.) #MASK 00:00:05 Masked IKZF1_HUMAN__Q13422 low relative conservation. (177 X added to 519aa seq.) #MASK 00:00:05 Masked ITF2_HUMAN__P15884 low relative conservation. (364 X added to 667aa seq.) #MASK 00:00:05 Masked KAT2B_HUMAN__Q92831 low relative conservation. (224 X added to 832aa seq.) #MASK 00:00:05 Masked LCORL_HUMAN__Q8N3X6 low relative conservation. (248 X added to 602aa seq.) #MASK 00:00:05 Masked LCOR_HUMAN__Q96JN0 low relative conservation. (144 X added to 433aa seq.) #GOPHER 00:00:05 Running GOPHER on MDS1_HUMAN__Q13465 #SYS 00:00:05 /share/apps/blast+/2.2.29/bin/blastp -query /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/HUMAN/BLAST/Q13465.qry -db /srv/slimsuite/data/orthdb/qfo_ref.2015-04/qfo_ref.2015-04.Eukaryota.fas -out /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/HUMAN/BLAST/Q13465.blast -seg yes -comp_based_stats T -soft_masking true -evalue 1.000000e-04 -num_descriptions 1000 -num_alignments 0 #INDEX 00:00:09 Indexed "Hit" on "Hit": 25 unique; 0 missing entries #QRY 00:00:09 WARNING: Query protein MDS1_HUMAN__Q13465 not (hit) in search database! #QRY 00:00:09 Query sequence MDS1_HUMAN__Q13465 added to BLAST Hits #QRY 00:00:09 Query Sequence = MDS1_HUMAN__Q13465 (169 AA). #FAS 00:00:09 26 Sequences output to /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/HUMAN/ORTH/Q13465.full.fas. #DB 00:00:09 /share/apps/blast+/2.2.29/bin/makeblastdb -in "/srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/HUMAN/ORTH/Q13465.full.fas" -out "/srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/HUMAN/ORTH/Q13465.full.fas" -title "/srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/HUMAN/ORTH/Q13465.full.fas" -parse_seqids -dbtype prot #SYS 00:00:09 /share/apps/blast+/2.2.29/bin/blastp -query /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/HUMAN/BLAST/Q13465.qry -db /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/HUMAN/ORTH/Q13465.full.fas -out /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/HUMAN/ORTH/Q13465.orth.blast -seg no -comp_based_stats F -soft_masking true -evalue 1.000000e+01 -num_descriptions 26 -num_alignments 26 #SIM 00:00:10 MDS1_HUMAN__Q13465: 10 of 36 hits failed to meet Min. Similarity threshold (GABLAMO Sim 40.00%) - removed. #SIM 00:00:10 MDS1_HUMAN__Q13465: 10 best hits for species. #PARA 00:00:10 MDS1_HUMAN__Q13465: 2 paralogues to consider. #FAS 00:00:10 10 Sequences output to /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/HUMAN/ORTH/Q13465.minsim.fas. #FAS 00:00:10 2 Sequences output to /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/HUMAN/PARA/Q13465.para.fas. #DB 00:00:10 /share/apps/blast+/2.2.29/bin/makeblastdb -in "/srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/HUMAN/ORTH/Q13465.minsim.fas" -out "/srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/HUMAN/ORTH/Q13465.minsim.fas" -title "/srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/HUMAN/ORTH/Q13465.minsim.fas" -parse_seqids -dbtype prot #SYS 00:00:10 /share/apps/blast+/2.2.29/bin/blastp -query /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/HUMAN/PARA/Q13465.para.fas -db /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/HUMAN/ORTH/Q13465.minsim.fas -out /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/HUMAN/PARA/Q13465.para.blast -seg no -comp_based_stats F -soft_masking true -evalue 1.000000e+01 -num_descriptions 26 -num_alignments 26 #FAS 00:00:10 7 Sequences output to /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/HUMAN/ORTH/Q13465.orth.fas. #SEQ 00:00:10 7 sequences loaded from /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/HUMAN/ORTH/Q13465.orth.fas (Format: fas). #NR 00:00:10 No duplicate AccNum detected. #FAS 00:00:10 7 Sequences output to /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/HUMAN/ORTH/Q13465.orth.fas. #ALN 00:00:10 Clustal Omega alignment: /share/apps/clustalo/1.2.1/bin/clustalo -i /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/HUMAN/ORTH/Q13465.orth.fas -o /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/HUMAN/ORTH/Q13465.orth.aln --outfmt=clu #SEQ 00:00:10 7 sequences loaded from /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/HUMAN/ORTH/Q13465.orth.aln (Format: aln). #NR 00:00:10 No duplicate AccNum detected. #MAP 00:00:10 Aligned sequences successfully mapped onto originals #FAS 00:00:10 7 Sequences output to /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/HUMAN/clustaloALN/Q13465.orthaln.fas. #SEQ 00:00:10 7 sequences loaded from /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/HUMAN/clustaloALN/Q13465.orthaln.fas (Format: fas). #QRY 00:00:10 Query Sequence = MDS1_HUMAN__Q13465 (169 AA). #ALN 00:00:10 Comparing 6 homologues for MDS1_HUMAN__Q13465. #MASK 00:00:10 Masked MDS1_HUMAN__Q13465 low relative conservation. (42 X added to 169aa seq.) #MASK 00:00:10 Masked NOL4L_HUMAN__Q96MY1 low relative conservation. (167 X added to 436aa seq.) #MASK 00:00:10 Masked NRIP1_HUMAN__P48552 low relative conservation. (544 X added to 1158aa seq.) #MASK 00:00:10 Masked RBBP5_HUMAN__Q15291 low relative conservation. (163 X added to 538aa seq.) #MASK 00:00:10 Masked SOBP_HUMAN__A7XYQ1 low relative conservation. (367 X added to 873aa seq.) #MASK 00:00:10 Masked ZN219_HUMAN__Q9P2Y4 low relative conservation. (251 X added to 722aa seq.) #REL 00:00:10 5,825 aa masked using relative conservation #RLC 00:00:10 rlc RLC score lists output to /srv/slimsuite/scratch/prod/slimfinder/15120900003/slimfinder.rlc.txt for 1 sequences. #FTMASK 00:00:10 FTMask: None #MASK 00:00:10 Masked CBX4_HUMAN__O00257 "low complexity" regions. (6 X added.) #MASK 00:00:10 Masked HIC1_HUMAN__Q14526 "low complexity" regions. (3 X added.) #MASK 00:00:10 Masked NRIP1_HUMAN__P48552 "low complexity" regions. (6 X added.) #MASK 00:00:10 Masked ZN219_HUMAN__Q9P2Y4 "low complexity" regions. (6 X added.) #MASK 00:00:10 MetMask: 11 N-terminal Ms masked #MASK 00:00:10 Masked SOBP_HUMAN__A7XYQ1 position-specific AAs. (1 X added.) #MASK 00:00:10 slimfinder: Masking of input sequences complete. #SPACE 00:00:10 Motif Space, 2 positions: 1,200 motifs #SPACE 00:00:10 Motif Space, 3 positions: 72,000 motifs #SPACE 00:00:10 Motif Space, 4 positions: 4,320,000 motifs #SPACE 00:00:10 Motif Space, 5 positions: 259,200,000 motifs #DIM 00:00:10 Read dimers from 20 seq: 1,181 dimers #DIM 00:00:10 Reducing dimers: 1,063 >= 2 of 16 UPC #SLIM 00:00:10 Selecting 2aa SLiMs: 1,063 >= 2 of 16 UPC #AMB 00:00:10 Adding Wildcard ambiguity: 100.0% (0 amb motifs) #AMB 00:00:10 Adding Degeneracy ambiguity: 100.0% (0 amb motifs) #SLIM 00:00:22 Extending 3aa SLiMs >= 2 of 16 UPC: 3,794 SLiMs #AMB 00:00:23 Adding Wildcard ambiguity: 100.0% (1,095 amb motifs) #AMB 00:00:24 Adding Degeneracy ambiguity: 100.0% (1,634 amb motifs) #SLIM 00:00:39 Extending 4aa SLiMs >= 2 of 16 UPC: 807 SLiMs #AMB 00:00:39 Adding Wildcard ambiguity: 100.0% (62 amb motifs) #AMB 00:00:39 Adding Degeneracy ambiguity: 100.0% (42 amb motifs) #SLIM 00:00:43 Extending 5aa SLiMs >= 2 of 16 UPC: 126 SLiMs #AMB 00:00:43 Adding Wildcard ambiguity: 100.0% (1 amb motifs) #AMB 00:00:43 Adding Degeneracy ambiguity: 100.0% (2 amb motifs) #SLIM 00:00:43 8,626 SLiMs >= 2 of 16 UPC #SAVE 00:00:44 SLiMFinder Intermediate saved as /srv/slimsuite/scratch/prod/slimfinder/15120900003/slimfinder.l5w2o2a3.FreqConsDisComp-5-8.pickle (Python pickle). #GZIP 00:00:44 /srv/slimsuite/scratch/prod/slimfinder/15120900003/slimfinder.l5w2o2a3.FreqConsDisComp-5-8.pickle zipped. #SLIM 00:00:44 Filtering 8,626 SLiMs: 3,678 retained. #PROB 00:00:46 Calculating [Sig] SLiM Probabilities (Sig<=0.10) complete: 8 ranked SLiMs. #COMB 00:00:46 Combined Occurrence Attributes complete. #CLOUD 00:00:46 Making "Motif Clouds" for 8 Sig Motifs: 3 Clouds #SLIM 00:00:46 Cloud 1 (D..[IL]DL|DL[ST].[KR]|P[IL]DL|P.DL|P.DL..[KR]|P.DLS.[KR]) SLiMMaker: [PV].DL #FREQ 00:00:46 SLiMMaker SLiM matches 16 of 18 sequences (88.9%). #SLIM 00:00:46 Cloud 2 (V.{0,2}QL) SLiMMaker: V[LQ][LQ] #FREQ 00:00:46 SLiMMaker SLiM matches 5 of 9 sequences (55.6%). #SLIM 00:00:46 Cloud 3 (I.D..F) SLiMMaker: I.D..F #FREQ 00:00:46 SLiMMaker SLiM matches 4 of 4 sequences (100.0%). #RANK 00:00:46 Rank calculations complete #CLOUD 00:00:46 Motif cloud data output to /srv/slimsuite/scratch/prod/slimfinder/15120900003/slimfinder.l5w2o2a3.CtBP1-ConsMask.cloud.txt for 3 clouds. #FAS 00:00:46 20 Sequences output to /srv/slimsuite/scratch/prod/slimfinder/15120900003/slimfinder.l5w2o2a3.CtBP1-ConsMask.masked.fas. #FAS 00:00:47 60 Sequences output to /srv/slimsuite/scratch/prod/slimfinder/15120900003/slimfinder.l5w2o2a3.CtBP1-ConsMask.mapping.fas. #ALN 00:00:47 Constructing motif alignments: 8 motifs & 15 seqs.: 100.0%. #FAS 00:00:47 19 Sequences output to /srv/slimsuite/scratch/prod/slimfinder/15120900003/slimfinder.l5w2o2a3.CtBP1-ConsMask.motifaln.fas. #ALN 00:00:47 Constructing motif alignments: 8 motifs & 15 seqs.: 100.0%. #FAS 00:00:47 19 Sequences output to /srv/slimsuite/scratch/prod/slimfinder/15120900003/slimfinder.l5w2o2a3.CtBP1-ConsMask.maskaln.fas. #OCC 00:00:47 Occurrence data output for 56 motif occurrences. #RES 00:00:47 SLiMFinder results output to /srv/slimsuite/scratch/prod/slimfinder/15120900003/slimfinder.csv and /srv/slimsuite/scratch/prod/slimfinder/15120900003/slimfinder.occ.csv. #RES 00:00:47 Additional dataset results output to /srv/slimsuite/scratch/prod/slimfinder/15120900003/slimfinder.* #END 00:00:47 SLiMFinder server run ended (Finished!): see log file for details. #WARN 00:00:47 1 warning messages: check log for details. #LOG 00:00:47 SLiMFinder V5.2.3 End: Wed Dec 9 00:30:14 2015 #JOBID 00:00:47 15120900003 #REST 00:00:47 URL for future retrieval: http://rest.slimsuite.unsw.edu.au/retrieve&jobid=15120900003&rest=format&password=None