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shahab-sarmashghi / RESPECT

Estimating repeat spectra and genome length from low-coverage genome skims

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due I need to install the program all over again if the academic license for Gurobi expires?

AntonioBaeza opened this issue · comments

commented

I assume this is related to the expired license,
due I need to install the program all over again if the academic license for Gurobi expires?
thanks!

(respect) ant@hillary:/RESPECT$ respect -d dataTURTLE/ -I dataTURTLE/hist_info.txt -N 10 --debug
2022-07-13 20:38:38,128 WARNING:dataTURTLE/hist_info.txt does not have valid extension; it's skipped
2022-07-13 20:38:38,131 WARNING:/home/ant/RESPECT/dataTURTLE/reads45.hist is missing from the histogram info file; it's skipped
2022-07-13 20:38:38,132 WARNING:/home/ant/RESPECT/dataTURTLE/reads27.hist is missing from the histogram info file; it's skipped
2022-07-13 20:38:38,132 WARNING:/home/ant/RESPECT/dataTURTLE/reads48.hist is missing from the histogram info file; it's skipped
2022-07-13 20:38:38,132 WARNING:/home/ant/RESPECT/dataTURTLE/reads36.hist is missing from the histogram info file; it's skipped
2022-07-13 20:38:38,132 WARNING:/home/ant/RESPECT/dataTURTLE/reads33.hist is missing from the histogram info file; it's skipped
2022-07-13 20:38:38,132 WARNING:/home/ant/RESPECT/dataTURTLE/reads39.hist is missing from the histogram info file; it's skipped
2022-07-13 20:38:38,132 WARNING:/home/ant/RESPECT/dataTURTLE/reads24.hist is missing from the histogram info file; it's skipped
2022-07-13 20:38:38,132 WARNING:/home/ant/RESPECT/dataTURTLE/reads51.hist is missing from the histogram info file; it's skipped
2022-07-13 20:38:38,132 WARNING:/home/ant/RESPECT/dataTURTLE/reads42.hist is missing from the histogram info file; it's skipped
2022-07-13 20:38:38,132 WARNING:/home/ant/RESPECT/dataTURTLE/reads30.hist is missing from the histogram info file; it's skipped
2022-07-13 20:38:38,132 INFO:Processing reads21.hist...
2022-07-13 20:38:38,633 INFO:Starting iterations to estimate parameters of reads21.hist
License expired 2022-01-13
2022-07-13 20:38:39,089 INFO:estimate_genome_skim_parameters finished in 0.7973372936248779 seconds
2022-07-13 20:38:39,089 ERROR:Error occurred when estimating parameters for /home/ant/RESPECT/dataTURTLE/reads21.hist; it's skipped
Traceback (most recent call last):
File "/home/ant/miniconda3/envs/respect/lib/python3.9/site-packages/respect-1.2.0-py3.9.egg/respect/paramter_estimator.py", line 342, in call
return self.estimate_genomic_parameters(*args, **kwargs)
File "/home/ant/miniconda3/envs/respect/lib/python3.9/site-packages/respect-1.2.0-py3.9.egg/respect/paramter_estimator.py", line 324, in estimate_genomic_parameters
self.estimate_genome_skim_parameters(spectra_number, error_norm, iterations_number, min_r1l, temperature)
File "/home/ant/miniconda3/envs/respect/lib/python3.9/site-packages/respect-1.2.0-py3.9.egg/respect/timer.py", line 68, in wrapper_timer
return func(*args, **kwargs)
File "/home/ant/miniconda3/envs/respect/lib/python3.9/site-packages/respect-1.2.0-py3.9.egg/respect/paramter_estimator.py", line 279, in estimate_genome_skim_parameters
optimizer.run_simulated_annealing(iterations_number, min_r1l, temperature)
File "/home/ant/miniconda3/envs/respect/lib/python3.9/site-packages/respect-1.2.0-py3.9.egg/respect/optimizer.py", line 395, in run_simulated_annealing
repeat_spectra_next = self.estimate_repeat_spectra(o[1:], poisson_matrix_next[1:, :])
File "/home/ant/miniconda3/envs/respect/lib/python3.9/site-packages/respect-1.2.0-py3.9.egg/respect/optimizer.py", line 335, in estimate_repeat_spectra
spectral_residuals = [1.0 * constrained_spectra[i] / norm(constrained_spectra[i:], ord=1) for i in range(
File "/home/ant/miniconda3/envs/respect/lib/python3.9/site-packages/respect-1.2.0-py3.9.egg/respect/optimizer.py", line 335, in
spectral_residuals = [1.0 * constrained_spectra[i] / norm(constrained_spectra[i:], ord=1) for i in range(
TypeError: 'NoneType' object is not subscriptable
2022-07-13 20:38:39,190 ERROR:Error occurred while trying to get estimated parameters for a sample
2022-07-13 20:38:39,198 INFO:Writing the results to the output files...
(respect) ant@hillary:/RESPECT$

commented

No, just obtain a new license from Gurobi website and activate it.

commented
commented

The error that you get after installing the new license, is it still about the expired license or something else? Did you remove/overwrite the old license? Because if you obtained a new license but saved it next to the old one, chances are Gurobi still sees the old license key instead of the new one.

commented
commented