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algo-cancer / ImmunoTyper-SR

Genotyping Immunoglobulin Heavy Chain Variable Genes using Short Read Data
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GurobiError: Model too large for size-limited license #9

Closed wbvguo closed 1 year ago

wbvguo commented 1 year ago

Dear tool developer,

I give the tool a test run on my bam file, and encounter the following error, have you met such error before? and could you please provide some guidance on how to solve it?

Traceback (most recent call last):
  File "xxx/.conda/envs/immunotyper-SR/bin/immunotyper-SR", line 8, in <module>
    sys.exit(main())
  File "xxx/.conda/envs/immunotyper-SR/lib/python3.8/site-packages/immunotyper/__main__.py", line 107, in main
    run_immunotyper(args.bam_path, args.ref, args.gene_type, args.hg37, args.output_dir, args.landmark_groups, args.landmarks_per_group, args.max_copy, args.stdev_coeff, args.seq_error_rate, args.write_cache_path, args.solver_time_limit, args.threads)
  File "xxx/.conda/envs/immunotyper-SR/lib/python3.8/site-packages/immunotyper/__main__.py", line 169, in run_immunotyper
    model.solve(timeLimit=solver_time_limit*3600, threads=threads, log_path=None)
  File "xxx/.conda/envs/immunotyper-SR/lib/python3.8/site-packages/immunotyper/lpinterface.py", line 167, in solve
    self.model.optimize()
  File "src/gurobipy/model.pxi", line 878, in gurobipy.Model.optimize
gurobipy.GurobiError: Model too large for size-limited license; visit https://www.gurobi.com/free-trial for a full license

Thanks,

michael-ford commented 1 year ago

Hey Wenbin,

ImmunoTyper-SR uses the Gurobi solver for its ILP model. Looks like you need to get a license as the free trial license it comes with is very limited - they have free full licenses for academic researchers. Once you set that up test it by running gurobi_cl. Let me know if you have any problems.

wbvguo commented 1 year ago

Thank you, close this issue now