Your GOPHER job has finished running and outputs have been parsed. Click on tabs to see server output. (Mouseover for description.)

The outfmt tab contains more information on the outputs. Click here for GOPHER help/documentation.

Content for individual tabs can be returned using &rest=X, where X is the tab name (e.g. &rest=log). Full output can be returned as text using &rest=full and parsed using SLiMParser:

python PATH/slimparser.py restin=JOBID restout=T [password=X] [restbase=X]

---

JobID 24042000000 (gopher) Finished.
IP:3.145.74.54
No queue.
gopher&acc=X&spcode=X
Run Started: 2024-04-20 11:41:05; PID=38227
Run finished: 2024-04-20 11:41:11

Results should be kept for at least one month but we cannot guarantee data storage.

Run with &rest=help for general options. Run with &rest=full to get full server output as text or &rest=format
for more user-friendly formatted output. Individual outputs can be identified/parsed using &rest=OUTFMT for:

OrthBLAST outputs

qry = Query file
blast = BLAST results file
blastid = BLAST hit ID file

Orthologue Identification

orthfas = Unaligned fasta file of GOPHER orthologues
orthid = ID list of GOPHER orthologues

Orthologue alignment

alnfas = Aligned fasta file of GOPHER orthologues

Orthologue tree

nwk = Tree of GOPHER orthologues in Newick format
tree = Tree of GOPHER orthologues in plain text format
png = Tree of GOPHER orthologues in PNG format

Paralogues

parafas = Unaligned fasta file of GOPHER paralogues
paraid = ID list of GOPHER paralogues
paralnfas = Aligned fasta file of GOPHER paralogues

Special GOPHER REST call

Note that individual outputs can be requested for single proteins using the special REST call:

http://rest.slimsuite.unsw.edu.au/gopher&acc=X&spcode=X&rest=X

If this protein has already been processed by GOPHER, the relevant output will be returned directly as plain
text. If not, a jobid will be returned, which will have the desired output once run.

Click here and save the page to download this output.

#~~#	#~+~~+~#	#~~#
#LOG	00:00:00	Activity Log for SLiMSuite V1.11.0: Sat Apr 20 11:41:05 2024
#DIR	00:00:00	Run from directory: /srv/slimsuite/logs/prod
#ARG	00:00:00	Commandline arguments: run ip=3.145.74.54 gopher&acc=X&spcode=X&jobid=24042000000
#VIO	00:00:00	Verbosity: -1; Interactivity: -1.
#PROG	00:00:00	GOPHER V3.5.4: Generation of Orthologous Proteins from Homology-based Estimation of Relationships
#CMD	00:00:00	Full GOPHER CmdList: proglog=F iucut=0.2 orthdb=qfo_ref.2019-04.Eukaryota.fas sourcedate=2015-04-15 maxgapx=3 usegopher=T protscores=T megablam=F restab=Search,Hit,Local qassemble=T combinedfas=T treeformats=nwk,text,png walltime=2.0 rest=format acc=X spcode=X jobid=24042000000 basefile=gopher
#ACC	00:00:00	No UniprotID list given but acc=X recognised: setting uniprotid=X
#PATH	00:00:00	Running from /srv/slimsuite/scratch/prod/gopher/24042000000
#MAP	00:00:00	New MapOut filename set: /srv/slimsuite/scratch/prod/gopher/24042000000/gopher.map.tdt
#ERR	00:00:05	UniProt entry "X" not found! Possibly withdrawn or demerged: (http_error_default line 518) HTTP Error 400: Bad Request
#URL	00:00:05	Extracting 1 AccNum from https://www.uniprot.org/uniprot/: 0 read, 0 extracted; 1 failed; 0 duplicates.
#ERR	00:00:05	Error in Gopher run(): (run line 437) Unable to generate input from UniprotID list.
#ERR	00:00:05	Problem with GOPHER run: (run line 437) Unable to generate input from UniprotID list.
#WARN	00:00:05	3 error messages! Check log for details.
#LOG	00:00:05	GOPHER V3.5.4 End: Sat Apr 20 11:41:11 2024
#JOBID	00:00:05	24042000000
#REST	00:00:05	URL for future retrieval: http://rest.slimsuite.unsw.edu.au/retrieve&jobid=24042000000&rest=format&password=None

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0 warning messages.

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#ERR	00:00:05	UniProt entry "X" not found! Possibly withdrawn or demerged:  (http_error_default line 518) HTTP Error 400: Bad Request  
#ERR	00:00:05	Error in Gopher run():  (run line 437) Unable to generate input from UniprotID list.  
#ERR	00:00:05	Problem with GOPHER run:  (run line 437) Unable to generate input from UniprotID list.