#~~# #~+~~+~# #~~# #LOG 00:00:00 Activity Log for SLiMSuite V1.5.2: Wed Dec 9 01:11:19 2015 #DIR 00:00:00 Run from directory: /srv/slimsuite/logs/prod #ARG 00:00:00 Commandline arguments: run ip=122.150.74.70 slimfinder&uniprotid=Q9H6U6,Q96MA1,O15409,Q14526,P09067,Q13422,O94818,Q96MY1,P48552,Q9NQ66,Q99708,Q15583,Q63HK5&dismask=T&consmask=T&featuremask=T&ambiguity=T&slimlen=5&maxwild=2&jobid=15120900013 #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 runid=15120900013 rest=format uniprotid=Q9H6U6,Q96MA1,O15409,Q14526,P09067,Q13422,O94818,Q96MY1,P48552,Q9NQ66,Q99708,Q15583,Q63HK5 dismask=T consmask=T featuremask=T ambiguity=T slimlen=5 maxwild=2 jobid=15120900013 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 Command ftmask=T converted to default ftmask=EM,DOMAIN,TRANSMEM. #WARN 00:00:00 NOTE: cloudfix=F. Be wary of ambiguity over-predictions. #URL 00:00:03 Extracting 13 AccNum from http://www.uniprot.org/uniprot/: 13 read & extracted; 0 failed; 0 duplicates. #DAT 00:00:04 Extracting entries from slimfinder.dat: 13 read, 13 extracted. #SEQ 00:00:04 13 sequences loaded from /srv/slimsuite/scratch/prod/slimfinder/15120900013/slimfinder.dat (Format: uniprot). #FAS 00:00:04 13 Sequences output to /srv/slimsuite/scratch/prod/slimfinder/15120900013/slimfinder.fas. #UPC 00:00:04 No UPC file found. #FAS 00:00:04 13 Sequences output to /srv/slimsuite/scratch/prod/slimfinder/15120900013/slimfinder.slimdb. #DICT 00:00:04 Made "short" seqName dictionary: 13 seq; 13 keys. #DB 00:00:04 /share/apps/blast+/2.2.29/bin/makeblastdb -in "/srv/slimsuite/scratch/prod/slimfinder/15120900013/slimfinder.slimdb" -out "/srv/slimsuite/scratch/prod/slimfinder/15120900013/slimfinder.slimdb" -title "/srv/slimsuite/scratch/prod/slimfinder/15120900013/slimfinder.slimdb" -parse_seqids -dbtype prot #SYS 00:00:04 /share/apps/blast+/2.2.29/bin/blastp -query /srv/slimsuite/scratch/prod/slimfinder/15120900013/slimfinder.slimdb -db /srv/slimsuite/scratch/prod/slimfinder/15120900013/slimfinder.slimdb -out /srv/slimsuite/scratch/prod/slimfinder/15120900013/slimfinder.self.blast -seg yes -comp_based_stats F -soft_masking true -evalue 1.000000e-04 -num_descriptions 13 -num_alignments 13 #INDEX 00:00:04 Indexed "Search" on "Query": 13 unique; 0 missing entries #CLUST 00:00:04 8 clusters generated from 13 keys (maxdis=1.00) #DICT 00:00:04 Made "short" seqName dictionary: 13 seq; 13 keys. #MST 00:00:04 MST for 13 sequences = 12.111. #UP 00:00:04 slimfinder: 13 Seq; 8 UPC; 12.111 MST; blaste=1.00e-04, blastcf=F, blastf=T #MAT 00:00:04 slimfinder GABLAM Distance matrix out to /srv/slimsuite/scratch/prod/slimfinder/15120900013/slimfinder.dis.tdt (text format). #MIN 00:00:04 AmbOcc 0.05 & 8 UP => AmbOcc 2 UPC. #MIN 00:00:04 MinOcc 0.05 & 8 UP => MinOcc 3 UPC. #DIS 00:00:04 Disorder score file: /srv/slimsuite/scratch/prod/slimfinder/15120900013/slimfinder.iupred.txt #MASK 00:00:04 BCAS3_HUMAN__Q9H6U6 masked 28 ordered regions. (308 X added.) #MASK 00:00:04 COM1_HUMAN__Q99708 masked 14 ordered regions. (46 X added.) #MASK 00:00:04 DMRTB_HUMAN__Q96MA1 masked 1 ordered regions. (43 X added.) #MASK 00:00:04 FOXP2_HUMAN__O15409 masked 14 ordered regions. (234 X added.) #MASK 00:00:04 HIC1_HUMAN__Q14526 masked 22 ordered regions. (221 X added.) #MASK 00:00:04 HXB5_HUMAN__P09067 masked 1 ordered regions. (35 X added.) #MASK 00:00:04 IKZF1_HUMAN__Q13422 masked 8 ordered regions. (110 X added.) #MASK 00:00:04 NOL4L_HUMAN__Q96MY1 masked 2 ordered regions. (27 X added.) #MASK 00:00:04 NOL4_HUMAN__O94818 masked 11 ordered regions. (71 X added.) #MASK 00:00:04 NRIP1_HUMAN__P48552 masked 10 ordered regions. (26 X added.) #MASK 00:00:04 PLCB1_HUMAN__Q9NQ66 masked 47 ordered regions. (436 X added.) #MASK 00:00:04 TGIF1_HUMAN__Q15583 masked 10 ordered regions. (57 X added.) #MASK 00:00:04 TSH3_HUMAN__Q63HK5 masked 16 ordered regions. (113 X added.) #DB 00:00:04 /srv/slimsuite/data/orthdb/qfo_ref.2015-04/qfo_ref.2015-04.Eukaryota.fas already formatted. (Force = False). #MASK 00:00:04 Masked BCAS3_HUMAN__Q9H6U6 low relative conservation. (326 X added to 928aa seq.) #MASK 00:00:04 Masked COM1_HUMAN__Q99708 low relative conservation. (377 X added to 897aa seq.) #MASK 00:00:04 Masked DMRTB_HUMAN__Q96MA1 low relative conservation. (164 X added to 342aa seq.) #MASK 00:00:04 Masked FOXP2_HUMAN__O15409 low relative conservation. (190 X added to 715aa seq.) #MASK 00:00:04 Masked HIC1_HUMAN__Q14526 low relative conservation. (238 X added to 733aa seq.) #MASK 00:00:04 Masked HXB5_HUMAN__P09067 low relative conservation. (109 X added to 269aa seq.) #MASK 00:00:04 Masked IKZF1_HUMAN__Q13422 low relative conservation. (177 X added to 519aa seq.) #MASK 00:00:04 Masked NOL4L_HUMAN__Q96MY1 low relative conservation. (167 X added to 436aa seq.) #MASK 00:00:04 Masked NOL4_HUMAN__O94818 low relative conservation. (285 X added to 638aa seq.) #MASK 00:00:04 Masked NRIP1_HUMAN__P48552 low relative conservation. (544 X added to 1158aa seq.) #MASK 00:00:04 Masked PLCB1_HUMAN__Q9NQ66 low relative conservation. (383 X added to 1216aa seq.) #MASK 00:00:04 Masked TGIF1_HUMAN__Q15583 low relative conservation. (159 X added to 401aa seq.) #MASK 00:00:04 Masked TSH3_HUMAN__Q63HK5 low relative conservation. (336 X added to 1081aa seq.) #REL 00:00:04 3,455 aa masked using relative conservation #FTMASK 00:00:04 FTMask: EM,DOMAIN,TRANSMEM #MASK 00:00:04 BCAS3_HUMAN__Q9H6U6 masked 0 features. (0 X added.) #MASK 00:00:04 COM1_HUMAN__Q99708 masked 0 features. (0 X added.) #MASK 00:00:04 DMRTB_HUMAN__Q96MA1 masked 0 features. (0 X added.) #MASK 00:00:04 FOXP2_HUMAN__O15409 masked 0 features. (0 X added.) #MASK 00:00:04 HIC1_HUMAN__Q14526 masked 1 features. (0 X added.) #MASK 00:00:04 HXB5_HUMAN__P09067 masked 0 features. (0 X added.) #MASK 00:00:04 IKZF1_HUMAN__Q13422 masked 0 features. (0 X added.) #MASK 00:00:04 NOL4L_HUMAN__Q96MY1 masked 0 features. (0 X added.) #MASK 00:00:04 NOL4_HUMAN__O94818 masked 0 features. (0 X added.) #MASK 00:00:04 NRIP1_HUMAN__P48552 masked 0 features. (0 X added.) #MASK 00:00:04 PLCB1_HUMAN__Q9NQ66 masked 3 features. (93 X added.) #MASK 00:00:04 TGIF1_HUMAN__Q15583 masked 0 features. (0 X added.) #MASK 00:00:04 TSH3_HUMAN__Q63HK5 masked 0 features. (0 X added.) #MASK 00:00:04 Masked DMRTB_HUMAN__Q96MA1 "low complexity" regions. (3 X added.) #MASK 00:00:04 Masked FOXP2_HUMAN__O15409 "low complexity" regions. (3 X added.) #MASK 00:00:04 Masked HIC1_HUMAN__Q14526 "low complexity" regions. (3 X added.) #MASK 00:00:04 Masked NRIP1_HUMAN__P48552 "low complexity" regions. (6 X added.) #MASK 00:00:04 Masked TGIF1_HUMAN__Q15583 "low complexity" regions. (9 X added.) #MASK 00:00:04 Masked TSH3_HUMAN__Q63HK5 "low complexity" regions. (7 X added.) #MASK 00:00:04 MetMask: 5 N-terminal Ms masked #MASK 00:00:04 Masked PLCB1_HUMAN__Q9NQ66 position-specific AAs. (1 X added.) #MASK 00:00:04 slimfinder: Masking of input sequences complete. #SPACE 00:00:04 Motif Space, 2 positions: 1,200 motifs #SPACE 00:00:04 Motif Space, 3 positions: 72,000 motifs #SPACE 00:00:04 Motif Space, 4 positions: 4,320,000 motifs #SPACE 00:00:04 Motif Space, 5 positions: 259,200,000 motifs #DIM 00:00:04 Read dimers from 13 seq: 1,142 dimers #DIM 00:00:04 Reducing dimers: 967 >= 2 of 8 UPC #SLIM 00:00:04 Selecting 2aa SLiMs: 967 >= 2 of 8 UPC #AMB 00:00:04 Adding Wildcard ambiguity: 100.0% (0 amb motifs) #AMB 00:00:04 Adding Degeneracy ambiguity: 100.0% (0 amb motifs) #SLIM 00:00:11 Extending 3aa SLiMs >= 2 of 8 UPC: 1,952 SLiMs #AMB 00:00:12 Adding Wildcard ambiguity: 100.0% (523 amb motifs) #AMB 00:00:12 Adding Degeneracy ambiguity: 100.0% (739 amb motifs) #SLIM 00:00:18 Extending 4aa SLiMs >= 2 of 8 UPC: 309 SLiMs #AMB 00:00:19 Adding Wildcard ambiguity: 100.0% (15 amb motifs) #AMB 00:00:19 Adding Degeneracy ambiguity: 100.0% (6 amb motifs) #SLIM 00:00:20 Extending 5aa SLiMs >= 2 of 8 UPC: 36 SLiMs #AMB 00:00:20 Adding Wildcard ambiguity: 100.0% (0 amb motifs) #AMB 00:00:20 Adding Degeneracy ambiguity: 100.0% (0 amb motifs) #SLIM 00:00:20 4,547 SLiMs >= 2 of 8 UPC #SAVE 00:00:20 SLiMFinder Intermediate saved as /srv/slimsuite/scratch/prod/slimfinder/15120900013/slimfinder.l5w2o2a3.FreqConsDisComp-5-8FT.pickle (Python pickle). #GZIP 00:00:20 /srv/slimsuite/scratch/prod/slimfinder/15120900013/slimfinder.l5w2o2a3.FreqConsDisComp-5-8FT.pickle zipped. #SLIM 00:00:20 Filtering 4,547 SLiMs: 1,595 retained. #PROB 00:00:21 Calculating [Sig] SLiM Probabilities (Sig<=0.10) complete: 2 ranked SLiMs. #COMB 00:00:21 Combined Occurrence Attributes complete. #CLOUD 00:00:21 Making "Motif Clouds" for 2 Sig Motifs: 1 Clouds #SLIM 00:00:21 Cloud 1 (P.DLS|DLS) SLiMMaker: [GP].DLS #FREQ 00:00:21 SLiMMaker SLiM matches 9 of 12 sequences (75.0%). #RANK 00:00:21 Rank calculations complete #CLOUD 00:00:21 Motif cloud data output to /srv/slimsuite/scratch/prod/slimfinder/15120900013/slimfinder.l5w2o2a3.15120900013.cloud.txt for 1 clouds. #FAS 00:00:21 13 Sequences output to /srv/slimsuite/scratch/prod/slimfinder/15120900013/slimfinder.l5w2o2a3.15120900013.masked.fas. #FAS 00:00:21 39 Sequences output to /srv/slimsuite/scratch/prod/slimfinder/15120900013/slimfinder.l5w2o2a3.15120900013.mapping.fas. #ALN 00:00:21 Constructing motif alignments: 2 motifs & 9 seqs.: 100.0%. #FAS 00:00:22 13 Sequences output to /srv/slimsuite/scratch/prod/slimfinder/15120900013/slimfinder.l5w2o2a3.15120900013.motifaln.fas. #ALN 00:00:22 Constructing motif alignments: 2 motifs & 9 seqs.: 100.0%. #FAS 00:00:22 13 Sequences output to /srv/slimsuite/scratch/prod/slimfinder/15120900013/slimfinder.l5w2o2a3.15120900013.maskaln.fas. #OCC 00:00:22 Occurrence data output for 18 motif occurrences. #RES 00:00:22 SLiMFinder results output to /srv/slimsuite/scratch/prod/slimfinder/15120900013/slimfinder.csv and /srv/slimsuite/scratch/prod/slimfinder/15120900013/slimfinder.occ.csv. #RES 00:00:22 Additional dataset results output to /srv/slimsuite/scratch/prod/slimfinder/15120900013/slimfinder.* #END 00:00:22 SLiMFinder server run ended (Finished!): see log file for details. #WARN 00:00:22 2 warning messages: check log for details. #LOG 00:00:22 SLiMFinder V5.2.3 End: Wed Dec 9 01:11:41 2015 #JOBID 00:00:22 15120900013 #REST 00:00:22 URL for future retrieval: http://rest.slimsuite.unsw.edu.au/retrieve&jobid=15120900013&rest=format&password=None