#~~# #~+~~+~# #~~# #LOG 00:00:00 Activity Log for SLiMSuite V1.5.2: Tue Dec 8 11:13:55 2015 #DIR 00:00:00 Run from directory: /srv/slimsuite/logs/prod #ARG 00:00:00 Commandline arguments: run ip=129.94.146.29 slimfinder&uniprotid=LIG_PCNA_PIPBox_1&dismask=T&jobid=15120800001 #VIO 00:00:00 Verbosity: -1; Interactivity: -1. #PROG 00:00:00 SLiMFinder V5.2.2: 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.2013-04.all.fas sourcedate=2014-05-28 walltime=0 runid=15120800001 rest=format uniprotid=LIG_PCNA_PIPBox_1.acc dismask=T jobid=15120800001 resfile=slimfinder.csv savespace=0 targz=F megaslim=seqin basefile=slimfinder #DB 00:00:00 /srv/slimsuite/data/orthdb/qfo_ref.2013-04/qfo_ref.2013-04.all.fas already formatted. (Force = False). #DB 00:00:00 /srv/slimsuite/data/orthdb/qfo_ref.2013-04/qfo_ref.2013-04.all.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 00:00:06 Extracting 18 AccNum from http://www.uniprot.org/uniprot/: 18 read & extracted; 0 failed; 0 duplicates. #DAT 00:00:06 Extracting entries from slimfinder.dat: 18 read, 18 extracted. #SEQ 00:00:06 18 sequences loaded from /srv/slimsuite/scratch/prod/slimfinder/15120800001/slimfinder.dat (Format: uniprot). #FAS 00:00:06 18 Sequences output to /srv/slimsuite/scratch/prod/slimfinder/15120800001/slimfinder.fas. #UPC 00:00:06 No UPC file found. #FAS 00:00:06 18 Sequences output to /srv/slimsuite/scratch/prod/slimfinder/15120800001/slimfinder.slimdb. #DICT 00:00:06 Made "short" seqName dictionary: 18 seq; 18 keys. #DB 00:00:06 /share/apps/blast+/2.2.29/bin/makeblastdb -in "/srv/slimsuite/scratch/prod/slimfinder/15120800001/slimfinder.slimdb" -out "/srv/slimsuite/scratch/prod/slimfinder/15120800001/slimfinder.slimdb" -title "/srv/slimsuite/scratch/prod/slimfinder/15120800001/slimfinder.slimdb" -parse_seqids -dbtype prot #SYS 00:00:06 /share/apps/blast+/2.2.29/bin/blastp -query /srv/slimsuite/scratch/prod/slimfinder/15120800001/slimfinder.slimdb -db /srv/slimsuite/scratch/prod/slimfinder/15120800001/slimfinder.slimdb -out /srv/slimsuite/scratch/prod/slimfinder/15120800001/slimfinder.self.blast -seg yes -comp_based_stats F -soft_masking true -evalue 1.000000e-04 -num_descriptions 18 -num_alignments 18 #INDEX 00:00:07 Indexed "Search" on "Query": 18 unique; 0 missing entries #CLUST 00:00:07 9 clusters generated from 18 keys (maxdis=1.00) #DICT 00:00:07 Made "short" seqName dictionary: 18 seq; 18 keys. #MST 00:00:07 MST for 18 sequences = 15.196. #UP 00:00:07 slimfinder: 18 Seq; 8 UPC; 15.196 MST; blaste=1.00e-04, blastcf=F, blastf=T #MAT 00:00:07 slimfinder GABLAM Distance matrix out to /srv/slimsuite/scratch/prod/slimfinder/15120800001/slimfinder.dis.tdt (text format). #MIN 00:00:07 AmbOcc 0.05 & 8 UP => AmbOcc 2 UPC. #MIN 00:00:07 MinOcc 0.05 & 8 UP => MinOcc 3 UPC. #DIS 00:00:07 Disorder score file: /srv/slimsuite/scratch/prod/slimfinder/15120800001/slimfinder.iupred.txt #MASK 00:00:07 CDN1A_HUMAN__P38936 masked 7 ordered regions. (29 X added.) #MASK 00:00:07 DNLI1_HUMAN__P18858 masked 36 ordered regions. (338 X added.) #MASK 00:00:07 DNLI1_YEAST__P04819 masked 20 ordered regions. (341 X added.) #MASK 00:00:07 DNMT1_HUMAN__P26358 masked 44 ordered regions. (573 X added.) #MASK 00:00:07 DPOD3_HUMAN__Q15054 masked 5 ordered regions. (91 X added.) #MASK 00:00:07 DPOD3_YEAST__P47110 masked 2 ordered regions. (108 X added.) #MASK 00:00:07 DPOD3_SCHPO__P30261 masked 9 ordered regions. (105 X added.) #MASK 00:00:07 ERCC5_HUMAN__P28715 masked 16 ordered regions. (218 X added.) #MASK 00:00:07 FEN1_HUMAN__P39748 masked 8 ordered regions. (154 X added.) #MASK 00:00:07 FEN1_YEAST__P26793 masked 10 ordered regions. (166 X added.) #MASK 00:00:07 MSH3_YEAST__P25336 masked 23 ordered regions. (734 X added.) #MASK 00:00:07 MSH6_HUMAN__P52701 masked 51 ordered regions. (644 X added.) #MASK 00:00:07 MSH6_YEAST__Q03834 masked 51 ordered regions. (624 X added.) #MASK 00:00:07 RAD2_YEAST__P07276 masked 25 ordered regions. (247 X added.) #MASK 00:00:07 RFC1_YEAST__P38630 masked 27 ordered regions. (322 X added.) #MASK 00:00:07 RRM3_YEAST__P38766 masked 21 ordered regions. (415 X added.) #MASK 00:00:07 UNG_HUMAN__P13051 masked 11 ordered regions. (103 X added.) #MASK 00:00:07 UNG_YEAST__P12887 masked 15 ordered regions. (134 X added.) #FTMASK 00:00:07 FTMask: EM #MASK 00:00:07 CDN1A_HUMAN__P38936 masked 0 features. (0 X added.) #MASK 00:00:07 DNLI1_HUMAN__P18858 masked 0 features. (0 X added.) #MASK 00:00:07 DNLI1_YEAST__P04819 masked 0 features. (0 X added.) #MASK 00:00:07 DNMT1_HUMAN__P26358 masked 0 features. (0 X added.) #MASK 00:00:07 DPOD3_HUMAN__Q15054 masked 0 features. (0 X added.) #MASK 00:00:07 DPOD3_YEAST__P47110 masked 0 features. (0 X added.) #MASK 00:00:07 DPOD3_SCHPO__P30261 masked 0 features. (0 X added.) #MASK 00:00:07 ERCC5_HUMAN__P28715 masked 0 features. (0 X added.) #MASK 00:00:07 FEN1_HUMAN__P39748 masked 0 features. (0 X added.) #MASK 00:00:07 FEN1_YEAST__P26793 masked 0 features. (0 X added.) #MASK 00:00:07 MSH3_YEAST__P25336 masked 0 features. (0 X added.) #MASK 00:00:07 MSH6_HUMAN__P52701 masked 0 features. (0 X added.) #MASK 00:00:07 MSH6_YEAST__Q03834 masked 0 features. (0 X added.) #MASK 00:00:07 RAD2_YEAST__P07276 masked 0 features. (0 X added.) #MASK 00:00:07 RFC1_YEAST__P38630 masked 0 features. (0 X added.) #MASK 00:00:07 RRM3_YEAST__P38766 masked 0 features. (0 X added.) #MASK 00:00:07 UNG_HUMAN__P13051 masked 0 features. (0 X added.) #MASK 00:00:07 UNG_YEAST__P12887 masked 0 features. (0 X added.) #MASK 00:00:07 Masked DNLI1_HUMAN__P18858 "low complexity" regions. (17 X added.) #MASK 00:00:07 Masked DNLI1_YEAST__P04819 "low complexity" regions. (3 X added.) #MASK 00:00:07 Masked DNMT1_HUMAN__P26358 "low complexity" regions. (11 X added.) #MASK 00:00:07 Masked DPOD3_HUMAN__Q15054 "low complexity" regions. (10 X added.) #MASK 00:00:07 Masked ERCC5_HUMAN__P28715 "low complexity" regions. (21 X added.) #MASK 00:00:07 Masked FEN1_YEAST__P26793 "low complexity" regions. (3 X added.) #MASK 00:00:07 Masked MSH3_YEAST__P25336 "low complexity" regions. (5 X added.) #MASK 00:00:07 Masked MSH6_HUMAN__P52701 "low complexity" regions. (15 X added.) #MASK 00:00:07 Masked MSH6_YEAST__Q03834 "low complexity" regions. (11 X added.) #MASK 00:00:07 Masked RAD2_YEAST__P07276 "low complexity" regions. (10 X added.) #MASK 00:00:07 Masked RFC1_YEAST__P38630 "low complexity" regions. (11 X added.) #MASK 00:00:07 Masked RRM3_YEAST__P38766 "low complexity" regions. (3 X added.) #MASK 00:00:07 Masked UNG_HUMAN__P13051 "low complexity" regions. (3 X added.) #MASK 00:00:07 Masked UNG_YEAST__P12887 "low complexity" regions. (3 X added.) #MASK 00:00:07 MetMask: 18 N-terminal Ms masked #MASK 00:00:07 Masked DPOD3_HUMAN__Q15054 position-specific AAs. (1 X added.) #MASK 00:00:07 Masked MSH3_YEAST__P25336 position-specific AAs. (1 X added.) #MASK 00:00:07 Masked MSH6_YEAST__Q03834 position-specific AAs. (1 X added.) #MASK 00:00:07 slimfinder: Masking of input sequences complete. #SPACE 00:00:07 Motif Space, 2 positions: 1,200 motifs #SPACE 00:00:07 Motif Space, 3 positions: 72,000 motifs #SPACE 00:00:07 Motif Space, 4 positions: 4,320,000 motifs #SPACE 00:00:07 Motif Space, 5 positions: 259,200,000 motifs #DIM 00:00:07 Read dimers from 18 seq: 1,221 dimers #DIM 00:00:07 Reducing dimers: 1,111 >= 2 of 8 UPC #SLIM 00:00:07 Selecting 2aa SLiMs: 1,111 >= 2 of 8 UPC #AMB 00:00:07 Adding Wildcard ambiguity: 100.0% (0 amb motifs) #AMB 00:00:07 Adding Degeneracy ambiguity: 100.0% (0 amb motifs) #SLIM 00:00:31 Extending 3aa SLiMs >= 2 of 8 UPC: 12,854 SLiMs #AMB 00:00:35 Adding Wildcard ambiguity: 100.0% (6,028 amb motifs) #AMB 00:00:46 Adding Degeneracy ambiguity: 100.0% (8,966 amb motifs) #SLIM 00:01:50 Extending 4aa SLiMs >= 2 of 8 UPC: 8,495 SLiMs #AMB 00:01:53 Adding Wildcard ambiguity: 100.0% (1,884 amb motifs) #AMB 00:01:57 Adding Degeneracy ambiguity: 100.0% (1,729 amb motifs) #SLIM 00:02:33 Extending 5aa SLiMs >= 2 of 8 UPC: 2,158 SLiMs #AMB 00:02:34 Adding Wildcard ambiguity: 100.0% (58 amb motifs) #AMB 00:02:39 Adding Degeneracy ambiguity: 100.0% (21 amb motifs) #SLIM 00:02:39 43,304 SLiMs >= 2 of 8 UPC #SAVE 00:02:43 SLiMFinder Intermediate saved as /srv/slimsuite/scratch/prod/slimfinder/15120800001/slimfinder.l5w2o2a3.FreqDisComp-5-8FT.pickle (Python pickle). #GZIP 00:02:44 /srv/slimsuite/scratch/prod/slimfinder/15120800001/slimfinder.l5w2o2a3.FreqDisComp-5-8FT.pickle zipped. #SLIM 00:02:44 Filtering 43,304 SLiMs: 23,140 retained. #PROB 00:02:51 Calculating [Sig] SLiM Probabilities (Sig<=0.10) complete: 50 ranked SLiMs. #COMB 00:02:52 Combined Occurrence Attributes complete. #CLOUD 00:02:53 Making "Motif Clouds" for 50 Sig Motifs: 1 Clouds #SLIM 00:02:54 Cloud 1 (Q..[IL].SFF|Q.[ST]..SFF|Q.[ST][IL]..FF|Q.TL..FF|Q..L..FF|[ST][IL].SFF|TL.SFF|Q.[ST][IL].S.F|Q.[ST][IL].SF|Q..[IL]..FF|Q..I..FF..K|Q.T..SFF|[IL].SFF|TL.{0,1}S.{0,1}FF|Q..L.SFF|Q..I..FF.{1,2}K|TL..FF|Q..[IL].S.F|Q..[IL].SF|K..Q..[IL]..FF|[ST]..SFF|[KR]Q..L..FF|Q.TL..F|Q.TL.S.F|T..SFF|Q.TL.SF|[ST][IL]..FF|Q..I..FF|Q.[ST]..S.F|[KR]..TL..FF|Q.[ST]..SF|L.SFF|Q.T..S.F|I..FF.{1,2}K|Q.[ST][IL]..F|[KR]Q.TL..F|[ILM]..F[FY]|[IL]..FF|TL.S.F|TL.SF|I..FF..K|Q.SI..FF|Q.T..S.{0,1}F|L..FF|[ILMV]..F[FY]|I..FF|KQ..L..FF|Q..L..F|Q.T.{1,2}S.{0,1}FF|Q.T.{1,2}S.F) SLiMMaker: [RST][ILM]..F[FY] #FREQ 00:02:54 SLiMMaker SLiM matches 17 of 23 sequences (73.9%). #RANK 00:02:54 Rank calculations complete #CLOUD 00:02:54 Motif cloud data output to /srv/slimsuite/scratch/prod/slimfinder/15120800001/slimfinder.l5w2o2a3.15120800001.cloud.txt for 1 clouds. #FAS 00:02:54 18 Sequences output to /srv/slimsuite/scratch/prod/slimfinder/15120800001/slimfinder.l5w2o2a3.15120800001.masked.fas. #FAS 00:02:55 54 Sequences output to /srv/slimsuite/scratch/prod/slimfinder/15120800001/slimfinder.l5w2o2a3.15120800001.mapping.fas. #ALN 00:02:55 Constructing motif alignments: 50 motifs & 18 seqs.: 100.0%. #FAS 00:02:55 27 Sequences output to /srv/slimsuite/scratch/prod/slimfinder/15120800001/slimfinder.l5w2o2a3.15120800001.motifaln.fas. #ALN 00:02:56 Constructing motif alignments: 50 motifs & 18 seqs.: 100.0%. #FAS 00:02:56 27 Sequences output to /srv/slimsuite/scratch/prod/slimfinder/15120800001/slimfinder.l5w2o2a3.15120800001.maskaln.fas. #OCC 00:02:56 Occurrence data output for 357 motif occurrences. #RES 00:02:56 SLiMFinder results output to /srv/slimsuite/scratch/prod/slimfinder/15120800001/slimfinder.csv and /srv/slimsuite/scratch/prod/slimfinder/15120800001/slimfinder.occ.csv. #RES 00:02:56 Additional dataset results output to /srv/slimsuite/scratch/prod/slimfinder/15120800001/slimfinder.* #END 00:02:56 SLiMFinder server run ended (Finished!): see log file for details. #WARN 00:02:56 1 warning messages: check log for details. #LOG 00:02:56 SLiMFinder V5.2.2 End: Tue Dec 8 11:16:51 2015 #JOBID 00:02:56 15120800001 #REST 00:02:56 URL for future retrieval: http://rest.slimsuite.unsw.edu.au/retrieve&jobid=15120800001&rest=format&password=None