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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? #8

Closed AntonioBaeza closed 1 year ago

AntonioBaeza commented 2 years ago

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$

shahab-sarmashghi commented 2 years ago

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

AntonioBaeza commented 2 years ago

Dear Shahab. I did that, but still it does not work!

On Thu, Jul 14, 2022 at 2:58 PM Shahab Sarmashghi @.***> wrote:

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

— Reply to this email directly, view it on GitHub https://github.com/shahab-sarmashghi/RESPECT/issues/8#issuecomment-1184792006, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALIJRA2G7CDESODHTKLG3EDVUBPNFANCNFSM53QQGCIQ . You are receiving this because you authored the thread.Message ID: @.***>

-- J. Antonio Baeza

Associate Professor Department of Biological Sciences, Clemson University South Carolina, USA & Research Associate Smithsonian Marine Station at Fort Pierce, Florida, USA & Adjunct Faculty Universidad Catolica del Norte, Coquimbo, Chile

Email: @. & @. Website: http://baezaantonio.wix.com/baezalabclemson Website (CI-team): https://baezaantonio.wixsite.com/clemsonmitogenomics Website ResearchGate: https://www.researchgate.net/profile/J_Baeza/ Website SemanticScholar: https://www.semanticscholar.org/author/Juan-Antonio-Baeza/144723920 Website ScienceOpen: https://www.scienceopen.com/search#author/da87367c-ed52-40ed-93d4-ca81ebc8037d OSF Profile: https://osf.io/u9dea/

shahab-sarmashghi commented 2 years ago

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.

shahab-sarmashghi commented 1 year ago

Hi Antonio,

You do not need to install the whole program, just obtain a new license from Gurobi and activate it.

Best, Shahab

On Wed, Jul 13, 2022 at 8:45 PM AntonioBaeza @.***> wrote:

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) @.:/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) **@.***:/RESPECT$

— Reply to this email directly, view it on GitHub https://github.com/shahab-sarmashghi/RESPECT/issues/8, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEMUG3VTFTEAIAW5VT3B5X3VT5PLPANCNFSM53QQGCIQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

AntonioBaeza commented 1 year ago

Thanks. I never found the old license, so I just copied it in the respect conda environment. I need to find the right place to place it. I have been exploring most folders but no news yet. Thanks

On Thu, Jul 14, 2022 at 3:20 PM Shahab Sarmashghi @.***> wrote:

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.

— Reply to this email directly, view it on GitHub https://github.com/shahab-sarmashghi/RESPECT/issues/8#issuecomment-1184810864, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALIJRAYNGE2ICHW4S5S7C3TVUBSBLANCNFSM53QQGCIQ . You are receiving this because you authored the thread.Message ID: @.***>

-- J. Antonio Baeza

Associate Professor Department of Biological Sciences, Clemson University South Carolina, USA & Research Associate Smithsonian Marine Station at Fort Pierce, Florida, USA & Adjunct Faculty Universidad Catolica del Norte, Coquimbo, Chile

Email: @. & @. Website: http://baezaantonio.wix.com/baezalabclemson Website (CI-team): https://baezaantonio.wixsite.com/clemsonmitogenomics Website ResearchGate: https://www.researchgate.net/profile/J_Baeza/ Website SemanticScholar: https://www.semanticscholar.org/author/Juan-Antonio-Baeza/144723920 Website ScienceOpen: https://www.scienceopen.com/search#author/da87367c-ed52-40ed-93d4-ca81ebc8037d OSF Profile: https://osf.io/u9dea/