TypeError: 'NoneType' object is not subscriptable

[bistace]

Hello and thank you for developing RESPECT!

I am trying to run RESPECT on a set of public data (SRR17698145) but I am running into an error and don't know how to fix it. Could you please help me? Here is the complete log:

respect -i SRR17698145_1.fastq.gz SRR17698145_2.fastq.gz -o output --threads 24

2023-03-17 10:07:46,799 INFO:Processing SRR17698145_1.fastq.gz...
2023-03-17 10:12:13,826 INFO:compute_kmer_histogram finished in 241.29436254501343 seconds
2023-03-17 10:12:13,847 INFO:Processing SRR17698145_2.fastq.gz...
2023-03-17 10:16:12,393 INFO:compute_kmer_histogram finished in 208.6772701740265 seconds
2023-03-17 10:16:12,776 INFO:Starting iterations to estimate parameters of SRR17698145_1.fastq.gz
2023-03-17 10:16:12,790 INFO:Starting iterations to estimate parameters of SRR17698145_2.fastq.gz
2023-03-17 10:16:13,450 INFO:Set parameter WLSAccessID
2023-03-17 10:16:13,450 INFO:Set parameter WLSAccessID
2023-03-17 10:16:13,450 INFO:Set parameter WLSSecret
2023-03-17 10:16:13,450 INFO:Set parameter WLSSecret
2023-03-17 10:16:13,450 INFO:Set parameter LicenseID to value 945288
2023-03-17 10:16:13,450 INFO:Set parameter LicenseID to value 945288
2023-03-17 10:16:14,222 INFO:estimate_genome_skim_parameters finished in 1.7742846012115479 seconds
2023-03-17 10:16:14,223 ERROR:Error occurred when estimating parameters for /env/export/bigtmp2/ONT/test_respect/papaver_nudicaule/SRR17698145_1.fastq.gz; it's skipped
Traceback (most recent call last):
  File "/opt/conda/envs/respect/lib/python3.7/site-packages/respect-1.3.0-py3.7.egg/respect/paramter_estimator.py", line 344, in __call__
    return self.estimate_genomic_parameters(*args, **kwargs)
  File "/opt/conda/envs/respect/lib/python3.7/site-packages/respect-1.3.0-py3.7.egg/respect/paramter_estimator.py", line 326, in estimate_genomic_parameters
    self.estimate_genome_skim_parameters(spectra_number, error_norm, iterations_number, min_r1l, temperature)
  File "/opt/conda/envs/respect/lib/python3.7/site-packages/respect-1.3.0-py3.7.egg/respect/timer.py", line 68, in wrapper_timer
    return func(*args, **kwargs)
  File "/opt/conda/envs/respect/lib/python3.7/site-packages/respect-1.3.0-py3.7.egg/respect/paramter_estimator.py", line 281, in estimate_genome_skim_parameters
    optimizer.run_simulated_annealing(iterations_number, min_r1l, temperature)
  File "/opt/conda/envs/respect/lib/python3.7/site-packages/respect-1.3.0-py3.7.egg/respect/optimizer.py", line 395, in run_simulated_annealing
    repeat_spectra_next = self.estimate_repeat_spectra(o[1:], poisson_matrix_next[1:, :])
  File "/opt/conda/envs/respect/lib/python3.7/site-packages/respect-1.3.0-py3.7.egg/respect/optimizer.py", line 336, in estimate_repeat_spectra
    n_splines)]
  File "/opt/conda/envs/respect/lib/python3.7/site-packages/respect-1.3.0-py3.7.egg/respect/optimizer.py", line 335, in <listcomp>
    spectral_residuals = [1.0 * constrained_spectra[i] / norm(constrained_spectra[i:], ord=1) for i in range(
TypeError: 'NoneType' object is not subscriptable
2023-03-17 10:16:14,225 ERROR:Error occurred while trying to get estimated parameters for a sample
2023-03-17 10:16:14,248 INFO:estimate_genome_skim_parameters finished in 1.7997772693634033 seconds
2023-03-17 10:16:14,248 ERROR:Error occurred when estimating parameters for /env/export/bigtmp2/ONT/test_respect/papaver_nudicaule/SRR17698145_2.fastq.gz; it's skipped
Traceback (most recent call last):
  File "/opt/conda/envs/respect/lib/python3.7/site-packages/respect-1.3.0-py3.7.egg/respect/paramter_estimator.py", line 344, in __call__
    return self.estimate_genomic_parameters(*args, **kwargs)
  File "/opt/conda/envs/respect/lib/python3.7/site-packages/respect-1.3.0-py3.7.egg/respect/paramter_estimator.py", line 326, in estimate_genomic_parameters
    self.estimate_genome_skim_parameters(spectra_number, error_norm, iterations_number, min_r1l, temperature)
  File "/opt/conda/envs/respect/lib/python3.7/site-packages/respect-1.3.0-py3.7.egg/respect/timer.py", line 68, in wrapper_timer
    return func(*args, **kwargs)
  File "/opt/conda/envs/respect/lib/python3.7/site-packages/respect-1.3.0-py3.7.egg/respect/paramter_estimator.py", line 281, in estimate_genome_skim_parameters
    optimizer.run_simulated_annealing(iterations_number, min_r1l, temperature)
  File "/opt/conda/envs/respect/lib/python3.7/site-packages/respect-1.3.0-py3.7.egg/respect/optimizer.py", line 395, in run_simulated_annealing
    repeat_spectra_next = self.estimate_repeat_spectra(o[1:], poisson_matrix_next[1:, :])
  File "/opt/conda/envs/respect/lib/python3.7/site-packages/respect-1.3.0-py3.7.egg/respect/optimizer.py", line 336, in estimate_repeat_spectra
    n_splines)]
  File "/opt/conda/envs/respect/lib/python3.7/site-packages/respect-1.3.0-py3.7.egg/respect/optimizer.py", line 335, in <listcomp>
    spectral_residuals = [1.0 * constrained_spectra[i] / norm(constrained_spectra[i:], ord=1) for i in range(
TypeError: 'NoneType' object is not subscriptable
2023-03-17 10:16:14,249 ERROR:Error occurred while trying to get estimated parameters for a sample
2023-03-17 10:16:14,355 INFO:Writing the results to the output files...

[shahab-sarmashghi]

Hi, is Gurobi license working? If you have installed it before you still need to renew it (the same way you installed it) every few months. This seems like a license issue to me. If you run RESPECT with --debug you will get more information regarding the error

[bistace]

Hello, adding --debug did not change the output of RESPECT. For the license, I ran gurobi_cl and got the following output:

Set parameter WLSAccessID
Set parameter WLSSecret
Set parameter LicenseID to value 945288
Set parameter LogFile to value "gurobi.log"
Academic license - for non-commercial use only - registered to benjamin.istace@genoscope.cns.fr
Using license file /opt/gurobi.lic

[bistace]

In the function solve_constrained_lp_using_gurobi of optimizer.py, I see this block:

if model.status == gurobipy.GRB.Status.OPTIMAL:
                solution = model.getAttr('x', r)
                return np.array(list(solution.values()))

If the status is not set to gurobipy.GRB.Status.OPTIMAL, the function will not return anything and the constrained_spectra in the estimate_repeat_spectra function of optimizer.py will be set to None, which is indeed not indexable. Could this be a possibility?

[shahab-sarmashghi]

That is a possibility, but I haven't encountered that before running it on many samples. Does the code even reach to that point? You can add a print statement to test that.

What happens when you try to run RESPECT on the toy data provided with the repository?

[bistace]

Hello,

you were right, it was indeed a license problem. After requesting a named-user license instead of a WLS license, RESPECT runs fine on test data.

Thanks a lot for your help!