#~~# #~+~~+~# #~~# #LOG 00:00:00 Activity Log for SLiMSuite V1.5.2: Tue Dec 8 22:08:36 2015 #DIR 00:00:00 Run from directory: /srv/slimsuite/logs/prod #ARG 00:00:00 Commandline arguments: run ip=129.94.133.155 slimprob&uniprotid=E1A_ADE02&motifs=elm&jobid=15120800029 #VIO 00:00:00 Verbosity: -1; Interactivity: -1. #PROG 00:00:00 SLiMProb V2.2.5: Short Linear Motif Probability tool #CMD 00:00:00 Full SLiMProb 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 runid=15120800029 slimcalc=Cons,IUP,SA rest=format uniprotid=E1A_ADE02 motifs=elm2015.motifs jobid=15120800029 resfile=slimprob.csv savespace=0 targz=F megaslim=seqin basefile=slimprob #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). #SPLIT 00:00:00 Found /srv/slimsuite/data/motifs/elm2015.split.motifs. Will load instead. #MOT 00:00:01 292 motifs read from /srv/slimsuite/data/motifs/elm2015.split.motifs (292 lines): 292 retained. #ALPH 00:00:01 Alphabet: A C D E F G H I K L M N P Q R S T V W Y #URL 00:00:03 Extracting 1 AccNum from http://www.uniprot.org/uniprot/: 1 read, 1 extracted; 0 failed; 0 duplicates. #DAT 00:00:03 Extracting entries from slimprob.dat: 1 read, 1 extracted. #SEQ 00:00:03 1 sequences loaded from /srv/slimsuite/scratch/prod/slimprob/15120800029/slimprob.dat (Format: uniprot). #FAS 00:00:03 1 Sequences output to /srv/slimsuite/scratch/prod/slimprob/15120800029/slimprob.fas. #UPC 00:00:03 No UPC file found. #UP 00:00:03 slimprob: 1 Seq; 1 UPC; 1.000 MST; Single sequence #FTMASK 00:00:03 FTMask: None #SEARCH 00:00:03 1 sequences searched for 292 motifs: 125 occ. #SAVE 00:00:03 SLiMProb Intermediate saved as /srv/slimsuite/scratch/prod/slimprob/15120800029/slimprob.elm2015.split.FreqNoMask.pickle (Python pickle). #GZIP 00:00:03 /srv/slimsuite/scratch/prod/slimprob/15120800029/slimprob.elm2015.split.FreqNoMask.pickle zipped. #GOPHER 00:00:03 Running GOPHER on E1A_ADE02__P03254 #MKDIR 00:00:03 mkdir /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/ADE02 #MKDIR 00:00:03 mkdir /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/ADE02/BLAST #SYS 00:00:03 /share/apps/blast+/2.2.29/bin/blastp -query /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/ADE02/BLAST/P03254.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/ADE02/BLAST/P03254.blast -seg yes -comp_based_stats T -soft_masking true -evalue 1.000000e-04 -num_descriptions 1000 -num_alignments 0 #COMPF 00:00:10 E1A_ADE02__P03254 yielded no BLAST hits. Low complexity sequence? Will try with -F F #SYS 00:00:10 /share/apps/blast+/2.2.29/bin/blastp -query /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/ADE02/BLAST/P03254.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/ADE02/BLAST/P03254.blast -seg no -comp_based_stats F -soft_masking true -evalue 1.000000e-04 -num_descriptions 1000 -num_alignments 0 #QRY 00:00:19 E1A_ADE02__P03254 yielded no BLAST hits. Short sequence? #MKDIR 00:00:19 mkdir /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/ADE02/ORTH #MKDIR 00:00:19 mkdir /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/ADE02/PARA #QRY 00:00:19 Query sequence E1A_ADE02__P03254 added to BLAST Hits #QRY 00:00:19 Query Sequence = E1A_ADE02__P03254 (289 AA). #FAS 00:00:19 1 Sequences output to /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/ADE02/ORTH/P03254.full.fas. #DB 00:00:19 /share/apps/blast+/2.2.29/bin/makeblastdb -in "/srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/ADE02/ORTH/P03254.full.fas" -out "/srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/ADE02/ORTH/P03254.full.fas" -title "/srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/ADE02/ORTH/P03254.full.fas" -parse_seqids -dbtype prot #SYS 00:00:19 /share/apps/blast+/2.2.29/bin/blastp -query /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/ADE02/BLAST/P03254.qry -db /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/ADE02/ORTH/P03254.full.fas -out /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/ADE02/ORTH/P03254.orth.blast -seg no -comp_based_stats F -soft_masking true -evalue 1.000000e+01 -num_descriptions 1 -num_alignments 1 #SIM 00:00:19 E1A_ADE02__P03254: 0 of 1 hits failed to meet Min. Similarity threshold (GABLAMO Sim 40.00%) - removed. #SIM 00:00:19 E1A_ADE02__P03254: 0 best hits for species. #PARA 00:00:19 E1A_ADE02__P03254: 0 paralogues to consider. #FAS 00:00:19 1 Sequences output to /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/ADE02/ORTH/P03254.orth.fas. #MKDIR 00:00:19 mkdir /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/ADE02/clustaloALN #SEQ 00:00:19 1 sequences loaded from /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/ADE02/ORTH/P03254.orth.fas (Format: fas). #NR 00:00:19 No duplicate AccNum detected. #ALN 00:00:19 Less than 2 sequences - cannot align! #FAS 00:00:19 1 Sequences output to /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/ADE02/clustaloALN/P03254.orthaln.fas. #FAS 00:00:19 1 Sequences output to /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/ADE02/clustaloALN/P03254.orthaln.fas. #SEQ 00:00:19 1 sequences loaded from /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/ADE02/clustaloALN/P03254.orthaln.fas (Format: fas). #QRY 00:00:19 Query Sequence = E1A_ADE02__P03254 (289 AA). #ALN 00:00:19 Not enough sequences for E1A_ADE02__P03254 in /srv/slimsuite/data/gopher/qfo_ref.2015-04.Eukaryota/ADE02/clustaloALN/P03254.orthaln.fas. #ALN 00:00:19 No alignment file found for E1A_ADE02__P03254. #OCC 00:00:19 Processing 125 occurrences complete. #PROB 00:00:19 Calculating SLiM Probabilities complete. #COMB 00:00:19 Combined Occurrence Attributes complete. #OUT 00:00:20 Summary data for slimprob saved to /srv/slimsuite/scratch/prod/slimprob/15120800029/slimprob.csv #RES 00:00:20 SLiMProb results output to /srv/slimsuite/scratch/prod/slimprob/15120800029/slimprob.(occ.)csv and /srv/slimsuite/scratch/prod/slimprob/15120800029/slimprob.* #LOG 00:00:20 SLiMProb V2.2.5 End: Tue Dec 8 22:08:56 2015 #JOBID 00:00:20 15120800029 #REST 00:00:20 URL for future retrieval: http://rest.slimsuite.unsw.edu.au/retrieve&jobid=15120800029&rest=format&password=None