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view test-data/TOPP.log @ 7:0f60da9c484a draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
author galaxyp
date Sun, 13 Dec 2020 17:20:04 +0000
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2020-12-13 17:20:12 RTModel:1:: Warning: Using OLIGO kernel but out_oligo_params was not specified. Trying to write to: RTModel_2_output.tmp_additional_parameters
2020-12-13 17:20:12 RTModel:1:: Warning: Using OLIGO kernel but out_oligo_trainset was not specified. Trying to write to: RTModel_2_output.tmp_samples
2020-12-13 17:20:13 RTModel:1:: Writing to 'TOPP.log'
2020-12-13 17:20:13 RTModel:1:: Debug level (after ini file): 1
2020-12-13 17:20:13 RTModel:1:: Value of string option 'no_progress': 0
2020-12-13 17:20:13 RTModel:1:: Value of string option 'in_positive': 
2020-12-13 17:20:13 RTModel:1:: Value of string option 'in': RTModel_4_input.txt
2020-12-13 17:20:13 RTModel:1:: Value of string option 'out': RTModel_4_output.tmp
2020-12-13 17:20:13 RTModel:1:: Value of string option 'additive_cv': 0
2020-12-13 17:20:13 RTModel:1:: Value of string option 'cv:skip_cv': 0
2020-12-13 17:20:13 RTModel:1:: Value of double option 'total_gradient_time': 1.0
2020-12-13 17:20:13 RTModel:1:: Value of double option 'max_std': 10.0
2020-12-13 17:20:13 RTModel:1:: Value of string option 'svm_type': NU_SVR
2020-12-13 17:20:13 RTModel:1:: Value of string option 'kernel_type': OLIGO
2020-12-13 17:20:13 RTModel:1:: Value of double option 'c': 1.953125e-03
2020-12-13 17:20:13 RTModel:1:: Value of double option 'nu': 0.5
2020-12-13 17:20:13 RTModel:1:: Value of double option 'cv:c_start': 1.953125e-03
2020-12-13 17:20:13 RTModel:1:: Value of double option 'cv:c_step_size': 2.0
2020-12-13 17:20:13 RTModel:1:: Value of double option 'cv:c_stop': 1.953125e-03
2020-12-13 17:20:13 RTModel:1:: Value of double option 'cv:nu_start': 0.4
2020-12-13 17:20:13 RTModel:1:: Value of double option 'cv:nu_step_size': 1.2
2020-12-13 17:20:13 RTModel:1:: Value of double option 'cv:nu_stop': 0.4
2020-12-13 17:20:13 RTModel:1:: Value of int option 'border_length': 22
2020-12-13 17:20:13 RTModel:1:: Value of double option 'sigma': 1.0
2020-12-13 17:20:13 RTModel:1:: Value of int option 'k_mer_length': 1
2020-12-13 17:20:13 RTModel:1:: Value of double option 'cv:sigma_start': 5.0
2020-12-13 17:20:13 RTModel:1:: Value of double option 'cv:sigma_step_size': 1.221055
2020-12-13 17:20:13 RTModel:1:: Value of double option 'cv:sigma_stop': 5.0
2020-12-13 17:20:13 RTModel:1:: CV from sigma = 5.0 to sigma = 5.0 with step size 1.221055
2020-12-13 17:20:13 RTModel:1:: Value of int option 'cv:number_of_runs': 1
2020-12-13 17:20:13 RTModel:1:: Number of CV runs: 1
2020-12-13 17:20:13 RTModel:1:: Value of int option 'cv:number_of_partitions': 5
2020-12-13 17:20:13 RTModel:1:: Number of CV partitions: 5
2020-12-13 17:20:13 RTModel:1:: Value of string option 'first_dim_rt': 0
2020-12-13 17:20:13 RTModel:1:: Value of int option 'debug': 1
2020-12-13 17:20:13 RTModel:1:: 26 sequences for training, 26 labels for training
2020-12-13 17:20:13 RTModel:1:: Best parameters found in cross validation: C: 1.953125e-03 nu: 0.4 sigma: 5.0 with performance 0.63203189556678
2020-12-13 17:20:13 RTModel:1:: Value of string option 'out': RTModel_4_output.tmp
2020-12-13 17:20:13 RTModel:1:: Value of string option 'out_oligo_params': 
2020-12-13 17:20:13 RTModel:1:: Value of string option 'out_oligo_trainset': 
2020-12-13 17:20:13 RTModel:1:: Warning: Using OLIGO kernel but out_oligo_params was not specified. Trying to write to: RTModel_4_output.tmp_additional_parameters
2020-12-13 17:20:13 RTModel:1:: Warning: Using OLIGO kernel but out_oligo_trainset was not specified. Trying to write to: RTModel_4_output.tmp_samples
2020-12-13 17:20:23 PrecursorMassCorrector:1:: Did not find a MS1 scan to the MS/MS scan at RT=632.697998046875
2020-12-13 17:20:23 PrecursorMassCorrector:1:: Did not find a MS1 scan to the MS/MS scan at RT=632.697998046875
2020-12-13 17:20:23 PrecursorMassCorrector:1:: Did not find a MS1 scan to the MS/MS scan at RT=632.697998046875
2020-12-13 17:20:23 PrecursorMassCorrector:1:: Did not find a MS1 scan to the MS/MS scan at RT=638.775024414062045
2020-12-13 17:20:23 PrecursorMassCorrector:1:: Did not find a MS1 scan to the MS/MS scan at RT=638.775024414062045
2020-12-13 17:20:23 PrecursorMassCorrector:1:: Did not find a MS1 scan to the MS/MS scan at RT=638.775024414062045