#~~# #~+~~+~# #~~# #LOG 00:00:00 Activity Log for SLiMSuite V1.5.2: Wed Dec 9 00:47:09 2015 #DIR 00:00:00 Run from directory: /srv/slimsuite/logs/prod #ARG 00:00:00 Commandline arguments: run ip=122.150.74.70 qslimfinder&query=P03254&uniprotid=P0C7T5,P38398,O00257,Q12873,Q99708,Q13363,P35221,Q92769,Q14526,Q13422,P15884,Q92831,Q8N3X6,Q96JN0,Q13465,Q96MY1,P48552,Q15291,A7XYQ1,Q9P2Y4,Q8IX07,P03254&dismask=T&consmask=F&featuremask=F&ambiguity=T&slimlen=5&maxwild=2&jobid=15120900008 #VIO 00:00:00 Verbosity: -1; Interactivity: -1. #PROG 00:00:00 QSLiMFinder V2.1.1: Query Short Linear Motif Finder #CMD 00:00:00 Full QSLiMFinder 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=15120900008 rest=format query=P03254 uniprotid=P0C7T5,P38398,O00257,Q12873,Q99708,Q13363,P35221,Q92769,Q14526,Q13422,P15884,Q92831,Q8N3X6,Q96JN0,Q13465,Q96MY1,P48552,Q15291,A7XYQ1,Q9P2Y4,Q8IX07,P03254 dismask=T consmask=F featuremask=F ambiguity=T slimlen=5 maxwild=2 jobid=15120900008 resfile=qslimfinder.csv savespace=0 targz=F megaslim=seqin basefile=qslimfinder #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=F interpreted as empty FTMask list. #WARN 00:00:00 NOTE: cloudfix=F. Be wary of ambiguity over-predictions. #URL 00:00:04 Extracting 22 AccNum from http://www.uniprot.org/uniprot/: 22 read & extracted; 0 failed; 0 duplicates. #DAT 00:00:05 Extracting entries from qslimfinder.dat: 22 read, 22 extracted. #SEQ 00:00:05 22 sequences loaded from /srv/slimsuite/scratch/prod/qslimfinder/15120900008/qslimfinder.dat (Format: uniprot). #FAS 00:00:05 22 Sequences output to /srv/slimsuite/scratch/prod/qslimfinder/15120900008/qslimfinder.fas. #UPC 00:00:05 No UPC file found. #FAS 00:00:05 22 Sequences output to /srv/slimsuite/scratch/prod/qslimfinder/15120900008/qslimfinder.slimdb. #DICT 00:00:05 Made "short" seqName dictionary: 22 seq; 22 keys. #DB 00:00:05 /share/apps/blast+/2.2.29/bin/makeblastdb -in "/srv/slimsuite/scratch/prod/qslimfinder/15120900008/qslimfinder.slimdb" -out "/srv/slimsuite/scratch/prod/qslimfinder/15120900008/qslimfinder.slimdb" -title "/srv/slimsuite/scratch/prod/qslimfinder/15120900008/qslimfinder.slimdb" -parse_seqids -dbtype prot #SYS 00:00:05 /share/apps/blast+/2.2.29/bin/blastp -query /srv/slimsuite/scratch/prod/qslimfinder/15120900008/qslimfinder.slimdb -db /srv/slimsuite/scratch/prod/qslimfinder/15120900008/qslimfinder.slimdb -out /srv/slimsuite/scratch/prod/qslimfinder/15120900008/qslimfinder.self.blast -seg yes -comp_based_stats F -soft_masking true -evalue 1.000000e-04 -num_descriptions 22 -num_alignments 22 #INDEX 00:00:05 Indexed "Search" on "Query": 22 unique; 0 missing entries #CLUST 00:00:05 17 clusters generated from 22 keys (maxdis=1.00) #DICT 00:00:05 Made "short" seqName dictionary: 22 seq; 22 keys. #MST 00:00:05 MST for 22 sequences = 20.594. #UP 00:00:05 qslimfinder: 22 Seq; 17 UPC; 20.594 MST; blaste=1.00e-04, blastcf=F, blastf=T #MAT 00:00:05 qslimfinder GABLAM Distance matrix out to /srv/slimsuite/scratch/prod/qslimfinder/15120900008/qslimfinder.dis.tdt (text format). #QRY 00:00:05 Query Sequence = E1A_ADE02__P03254 (289 AA). #QRY 00:00:05 1 sequences mapped to focal group "Query" #FOCUS 00:00:05 Mapped 1 focal sequences in 1 group(s) #MIN 00:00:05 AmbOcc 0.05 & 17 UP => AmbOcc 2 UPC. #MIN 00:00:05 MinOcc 0.05 & 17 UP => MinOcc 3 UPC. #DIS 00:00:05 Disorder score file: /srv/slimsuite/scratch/prod/qslimfinder/15120900008/qslimfinder.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 E1A_ADE02__P03254 masked 7 ordered regions. (54 X added.) #MASK 00:00:05 FOG1_HUMAN__Q8IX07 masked 15 ordered regions. (245 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.) #FTMASK 00:00:05 FTMask: None #MASK 00:00:05 Masked ATX1L_HUMAN__P0C7T5 "low complexity" regions. (9 X added.) #MASK 00:00:05 Masked BRCA1_HUMAN__P38398 "low complexity" regions. (6 X added.) #MASK 00:00:05 Masked CBX4_HUMAN__O00257 "low complexity" regions. (21 X added.) #MASK 00:00:05 Masked CHD3_HUMAN__Q12873 "low complexity" regions. (36 X added.) #MASK 00:00:05 Masked COM1_HUMAN__Q99708 "low complexity" regions. (3 X added.) #MASK 00:00:05 Masked CTNA1_HUMAN__P35221 "low complexity" regions. (3 X added.) #MASK 00:00:05 Masked E1A_ADE02__P03254 "low complexity" regions. (3 X added.) #MASK 00:00:05 Masked FOG1_HUMAN__Q8IX07 "low complexity" regions. (34 X added.) #MASK 00:00:05 Masked HIC1_HUMAN__Q14526 "low complexity" regions. (33 X added.) #MASK 00:00:05 Masked ITF2_HUMAN__P15884 "low complexity" regions. (10 X added.) #MASK 00:00:05 Masked KAT2B_HUMAN__Q92831 "low complexity" regions. (19 X added.) #MASK 00:00:05 Masked LCORL_HUMAN__Q8N3X6 "low complexity" regions. (9 X added.) #MASK 00:00:05 Masked NOL4L_HUMAN__Q96MY1 "low complexity" regions. (14 X added.) #MASK 00:00:05 Masked NRIP1_HUMAN__P48552 "low complexity" regions. (6 X added.) #MASK 00:00:05 Masked RBBP5_HUMAN__Q15291 "low complexity" regions. (3 X added.) #MASK 00:00:05 Masked SOBP_HUMAN__A7XYQ1 "low complexity" regions. (23 X added.) #MASK 00:00:05 Masked ZN219_HUMAN__Q9P2Y4 "low complexity" regions. (35 X added.) #MASK 00:00:05 MetMask: 22 N-terminal Ms masked #MASK 00:00:05 Masked HDAC2_HUMAN__Q92769 position-specific AAs. (1 X added.) #MASK 00:00:05 Masked SOBP_HUMAN__A7XYQ1 position-specific AAs. (1 X added.) #MASK 00:00:05 qslimfinder: Masking of input sequences complete. #SPACE 00:00:05 Motif Space, 2 positions: 1,200 motifs #SPACE 00:00:05 Motif Space, 3 positions: 72,000 motifs #SPACE 00:00:05 Motif Space, 4 positions: 4,320,000 motifs #SPACE 00:00:05 Motif Space, 5 positions: 259,200,000 motifs #DIM 00:00:05 Read dimers from 22 seq: 1,246 dimers -> 407 Query dimers. #DIM 00:00:05 Reducing dimers: 1,183 >= 2 of 17 UPC #SPACE 00:00:05 Query Motif Space, 2 positions: 1,200 motifs -> 407 Query motifs #SLIM 00:00:05 Selecting 2aa SLiMs: 1,183 >= 2 of 17 UPC -> 405 of 407 query motifs #AMB 00:00:05 Adding Wildcard ambiguity: 100.0% (0 amb motifs) #AMB 00:00:05 Adding Degeneracy ambiguity: 100.0% (0 amb motifs) #SLIM 00:00:48 Extending 3aa SLiMs >= 2 of 17 UPC: 22,154 SLiMs #SPACE 00:00:48 Exact Query Motif Space, 3 positions: 72,000 motifs -> 1,703 Query motifs #AMB 00:00:49 Adding Wildcard ambiguity: 100.0% (1,026 amb motifs) #AMB 00:00:51 Adding Degeneracy ambiguity: 100.0% (1,794 amb motifs) #SLIM 00:03:11 Extending 4aa SLiMs >= 2 of 17 UPC: 23,594 SLiMs #SPACE 00:03:12 Exact Query Motif Space, 4 positions: 4,320,000 motifs -> 5,089 Query motifs #AMB 00:03:13 Adding Wildcard ambiguity: 100.0% (595 amb motifs) #AMB 00:03:14 Adding Degeneracy ambiguity: 100.0% (661 amb motifs) #SLIM 00:05:01 Extending 5aa SLiMs >= 2 of 17 UPC: 6,180 SLiMs #SPACE 00:05:06 Exact Query Motif Space, 5 positions: 259,200,000 motifs -> 14,667 Query motifs #AMB 00:05:06 Adding Wildcard ambiguity: 100.0% (64 amb motifs) #AMB 00:05:06 Adding Degeneracy ambiguity: 100.0% (12 amb motifs) #SLIM 00:05:06 57,263 SLiMs >= 2 of 17 UPC #SAVE 00:05:11 QSLiMFinder Intermediate saved as /srv/slimsuite/scratch/prod/qslimfinder/15120900008/qslimfinder.Ql5w2o2a3.FreqDisComp-5-8.pickle (Python pickle). #GZIP 00:05:12 /srv/slimsuite/scratch/prod/qslimfinder/15120900008/qslimfinder.Ql5w2o2a3.FreqDisComp-5-8.pickle zipped. #SLIM 00:05:13 Filtering 57,263 SLiMs: 5,088 retained. #PROB 00:05:15 Calculating [QSig] SLiM Probabilities (Sig<=0.10) complete: 6 ranked SLiMs. #COMB 00:05:16 Combined Occurrence Attributes complete. #CLOUD 00:05:16 Making "Motif Clouds" for 6 Sig Motifs: 1 Clouds #SLIM 00:05:16 Cloud 1 (P.DLS.[KR]|P[IL]DL|[IL]DLS.[KR]|P.DLS.K|P.DL[ST]|P[IL]DLS) SLiMMaker: P[IL]DL[ST] #FREQ 00:05:16 SLiMMaker SLiM matches 7 of 16 sequences (43.8%). #RANK 00:05:16 Rank calculations complete #CLOUD 00:05:16 Motif cloud data output to /srv/slimsuite/scratch/prod/qslimfinder/15120900008/qslimfinder.Ql5w2o2a3.15120900008.cloud.txt for 1 clouds. #FAS 00:05:16 22 Sequences output to /srv/slimsuite/scratch/prod/qslimfinder/15120900008/qslimfinder.Ql5w2o2a3.15120900008.masked.fas. #FAS 00:05:16 66 Sequences output to /srv/slimsuite/scratch/prod/qslimfinder/15120900008/qslimfinder.Ql5w2o2a3.15120900008.mapping.fas. #ALN 00:05:17 Constructing motif alignments: 6 motifs & 13 seqs.: 100.0%. #FAS 00:05:17 15 Sequences output to /srv/slimsuite/scratch/prod/qslimfinder/15120900008/qslimfinder.Ql5w2o2a3.15120900008.motifaln.fas. #ALN 00:05:17 Constructing motif alignments: 6 motifs & 13 seqs.: 100.0%. #FAS 00:05:17 15 Sequences output to /srv/slimsuite/scratch/prod/qslimfinder/15120900008/qslimfinder.Ql5w2o2a3.15120900008.maskaln.fas. #OCC 00:05:17 Occurrence data output for 43 motif occurrences. #RES 00:05:17 QSLiMFinder results output to /srv/slimsuite/scratch/prod/qslimfinder/15120900008/qslimfinder.csv and /srv/slimsuite/scratch/prod/qslimfinder/15120900008/qslimfinder.occ.csv. #RES 00:05:17 Additional dataset results output to /srv/slimsuite/scratch/prod/qslimfinder/15120900008/qslimfinder* #WARN 00:05:17 2 warning messages: check log for details. #LOG 00:05:17 QSLiMFinder V2.1.1 End: Wed Dec 9 00:52:27 2015 #JOBID 00:05:17 15120900008 #REST 00:05:17 URL for future retrieval: http://rest.slimsuite.unsw.edu.au/retrieve&jobid=15120900008&rest=format&password=None